rs590991

Variant names:

• chr6-116761419-T-C
• rs590991
• NM_001085480.3:c.390+558A>G

Variant summary

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

The ENST00000368557.6(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 ENST00000368557.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368557.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM162B	NM_001085480.3	MANE Select	c.390+558A>G		intron	N/A	NP_001078949.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM162B	ENST00000368557.6	TSL:1 MANE Select	c.390+558A>G		intron	N/A	ENSP00000357545.4

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

African (AFR) AF: 0.692 AC: 28569 AN: 41276

American (AMR) AF: 0.611 AC: 9279 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2273 AN: 3464

East Asian (EAS) AF: 0.521 AC: 2682 AN: 5144

South Asian (SAS) AF: 0.458 AC: 2203 AN: 4810

European-Finnish (FIN) AF: 0.432 AC: 4527 AN: 10482

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31772 AN: 67866

Other (OTH) AF: 0.577 AC: 1217 AN: 2108

Alfa AF: 0.488 Hom.: 9397

Bravo AF: 0.571

Asia WGS AF: 0.512 AC: 1781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.5
DANN	Benign	0.73
PhyloP100		0.55
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: rs590991; hg19: chr6-117082582; COSMIC: COSV63920737;