Variant chr6-112101444-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001033564.3(FAM229B):c.*657T>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 0.298 in 152,178 control chromosomes in the GnomAD database, including 7,149 homozygotes. 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: 𝑓 0.30 ( 7149 hom., cov: 33)

Exomes 𝑓: 0.17 ( 0 hom. )

Consequence

FAM229B
NM_001033564.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Variant links:

Genes affected

FAM229B (HGNC:33858): (family with sequence similarity 229 member B)

FAM229B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
FAM229B	NM_001033564.3 linkuse as main transcript	c.*657T>C	3_prime_UTR_variant	4/4	ENST00000368656.7	NP_001028736.1	Q4G0N7
FAM229B	XM_017011174.3 linkuse as main transcript	c.*657T>C	3_prime_UTR_variant	4/4		XP_016866663.1	Q4G0N7
FAM229B	XM_017011175.3 linkuse as main transcript	c.*657T>C	3_prime_UTR_variant	3/3		XP_016866664.1	Q4G0N7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM229B	ENST00000368656.7 linkuse as main transcript	c.*657T>C		3_prime_UTR_variant	4/4	1	NM_001033564.3	ENSP00000357645.2		Q4G0N7

Frequencies

GnomAD3 genomes

AF:

0.298

AC:

45347

AN:

152054

Hom.:

7136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.409

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.302

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.298

AC:

45404

AN:

152172

Hom.:

7149

Cov.:

AF XY:

0.291

AC XY:

21683

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.410

Gnomad4 AMR

AF:

0.226

Gnomad4 ASJ

AF:

0.303

Gnomad4 EAS

AF:

0.321

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.206

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.303

Alfa

AF:

0.282

Hom.:

1265

Bravo

AF:

0.308

Asia WGS

AF:

0.250

AC:

868

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.23

DANN

Benign

0.24

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over