rs753659

Positions:

• chr9-133590934-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

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 = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM163B	NM_001080515.3	c.-23-10688A>G		intron_variant		ENST00000673969.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM163B	ENST00000673969.1	c.-23-10688A>G		intron_variant			NM_001080515.3	P1

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

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.0667

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0148

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0585 Hom.: 310

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

Splicing

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

Publications

LitVar

Other links and lift over

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