rs753659

Variant names:

• chr9-133590934-T-C
• rs753659
• NM_001080515.3:c.-23-10688A>G

Variant summary

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

The NM_001080515.3(FAM163B):​c.-23-10688A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,276 control chromosomes in the GnomAD database, including 2,100 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 0.11 (2100 hom., cov: 33)
• Consequence: FAM163B NM_001080515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 1 publications found

Genes affected

FAM163B (HGNC:33277): (family with sequence similarity 163 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM163B	NM_001080515.3	c.-23-10688A>G		intron_variant	Intron 1 of 2	ENST00000673969.1	NP_001073984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM163B	ENST00000673969.1	c.-23-10688A>G		intron_variant	Intron 1 of 2		NM_001080515.3	ENSP00000501259.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16635 AN: 152158 Hom.: 2099 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.109 AC: 16652 AN: 152276 Hom.: 2100 Cov.: 33 AF XY: 0.106 AC XY: 7864 AN XY: 74460

African (AFR) AF: 0.307 AC: 12762 AN: 41534

American (AMR) AF: 0.0667 AC: 1021 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4830

European-Finnish (FIN) AF: 0.0148 AC: 157 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0298 AC: 2030 AN: 68018

Other (OTH) AF: 0.103 AC: 217 AN: 2116

Alfa AF: 0.0466 Hom.: 782

Bravo AF: 0.123

Asia WGS AF: 0.0250 AC: 85 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	0.54
PhyloP100		-0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs753659; hg19: chr9-136456056; COSMIC: COSV72395702;