20-56534248-C-T

Variant names:

• chr20-56534248-C-T
• rs6024938
• NM_001013646.4:c.249+658C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001013646.4(FAM209B):​c.249+658C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,058 control chromosomes in the GnomAD database, including 36,459 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 0.68 (36459 hom., cov: 32)
• Consequence: FAM209B NM_001013646.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 12 publications found

Genes affected

FAM209B (HGNC:16101): (family with sequence similarity 209 member B) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013646.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM209B	NM_001013646.4	MANE Select	c.249+658C>T		intron	N/A	NP_001013668.2	Q5JX69

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM209B	ENST00000371325.1	TSL:1 MANE Select	c.249+658C>T		intron	N/A	ENSP00000360376.1	Q5JX69

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102946 AN: 151938 Hom.: 36405 Cov.: 32

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.650

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.678 AC: 103047 AN: 152058 Hom.: 36459 Cov.: 32 AF XY: 0.669 AC XY: 49688 AN XY: 74314

African (AFR) AF: 0.898 AC: 37304 AN: 41524

American (AMR) AF: 0.555 AC: 8478 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3472

East Asian (EAS) AF: 0.554 AC: 2866 AN: 5172

South Asian (SAS) AF: 0.505 AC: 2433 AN: 4814

European-Finnish (FIN) AF: 0.546 AC: 5760 AN: 10544

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42054 AN: 67956

Other (OTH) AF: 0.649 AC: 1369 AN: 2110

Alfa AF: 0.632 Hom.: 117557

Bravo AF: 0.685

Asia WGS AF: 0.507 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6024938; hg19: chr20-55109304;