Genetic Variant BANF1:c.*143T>C (chr11-66003915-T-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_003860.4(BANF1):c.*143T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000028 in 1,071,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0000028 ( 0 hom. )

Consequence

BANF1
NM_003860.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.45

Publications

1 publications found

Variant links:

Genes affected

BANF1 (HGNC:17397): (BAF nuclear assembly factor 1) The protein encoded by this gene was first identified by its ability to protect retroviruses from intramolecular integration and therefore promote intermolecular integration into the host cell genome. The protein forms a homodimer which localizes to both the nucleus and cytoplasm and is specifically associated with chromosomes during mitosis. This protein binds to double stranded DNA in a non-specific manner and also binds to LEM-domain containing proteins of the nuclear envelope. This protein is thought to facilitate nuclear reassembly by binding with both DNA and inner nuclear membrane proteins and thereby recruit chromatin to the nuclear periphery. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Jan 2009]

BANF1 Gene-Disease associations (from GenCC):

Nestor-Guillermo progeria syndrome
Inheritance: AR, Unknown Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

BANF1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003860.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BANF1	NM_003860.4	MANE Select	c.*143T>C	3_prime_UTR	Exon 3 of 3	NP_003851.1	O75531
BANF1	NM_001143985.2		c.*143T>C	3_prime_UTR	Exon 3 of 3	NP_001137457.1
BANF1	NM_001440618.1		c.*143T>C	3_prime_UTR	Exon 3 of 3	NP_001427547.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BANF1	ENST00000312175.7	TSL:1 MANE Select	c.*143T>C	3_prime_UTR	Exon 3 of 3	ENSP00000310275.2	O75531
BANF1	ENST00000445560.6	TSL:1	c.*143T>C	3_prime_UTR	Exon 3 of 3	ENSP00000416128.2	O75531
BANF1	ENST00000533166.5	TSL:2	c.*143T>C	3_prime_UTR	Exon 3 of 3	ENSP00000433760.1	O75531

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000280

AC:

AN:

1071554

Hom.:

Cov.:

AF XY:

0.00000372

AC XY:

AN XY:

537070

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24168

American (AMR)

AF:

0.00

AC:

AN:

29558

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21810

East Asian (EAS)

AF:

0.00

AC:

AN:

33902

South Asian (SAS)

AF:

0.00

AC:

AN:

70678

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36674

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3372

European-Non Finnish (NFE)

AF:

0.00000373

AC:

AN:

804798

Other (OTH)

AF:

0.00

AC:

AN:

46594

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

3.4

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over