rs590991

chr6-116761419-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001085480.3(FAM162B):c.390+558A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,550 control chromosomes in the GnomAD database, including 23,693 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 0.55 (23693 hom., cov: 30)
• Consequence: FAM162B NM_001085480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

Genes affected

FAM162B (HGNC:21549): (family with sequence similarity 162 member B) Predicted to be integral component of membrane. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM162B	NM_001085480.3	c.390+558A>G		intron_variant		ENST00000368557.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM162B	ENST00000368557.6	c.390+558A>G		intron_variant		1	NM_001085480.3	P1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83140 AN: 151434 Hom.: 23655 Cov.: 30

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.549 AC: 83237 AN: 151550 Hom.: 23693 Cov.: 30 AF XY: 0.547 AC XY: 40502 AN XY: 74048

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.577

Alfa AF: 0.499 Hom.: 6018

Bravo AF: 0.571

Asia WGS AF: 0.512 AC: 1781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.5
Dann	Benign	0.73

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: rs590991; hg19: chr6-117082582; COSMIC: COSV63920737;