20-56534248-C-T

Position:

• chr20-56534248-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM209B	NM_001013646.4	c.249+658C>T		intron_variant		ENST00000371325.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM209B	ENST00000371325.1	c.249+658C>T		intron_variant		1	NM_001013646.4	P1

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

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.649

Alfa AF: 0.619 Hom.: 49256

Bravo AF: 0.685

Asia WGS AF: 0.507 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs6024938; hg19: chr20-55109304;