chr9-133597376-G-C

Position:

• chr9-133597376-G-C

Variant summary

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

The NM_001080515.3(FAM163B):​c.-24+11701C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,018 control chromosomes in the GnomAD database, including 33,955 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 0.66 (33955 hom., cov: 32)
• Consequence: FAM163B NM_001080515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM163B	NM_001080515.3	c.-24+11701C>G		intron_variant		ENST00000673969.1	NP_001073984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM163B	ENST00000673969.1	c.-24+11701C>G		intron_variant			NM_001080515.3	ENSP00000501259	P1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99493 AN: 151902 Hom.: 33924 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.655 AC: 99574 AN: 152018 Hom.: 33955 Cov.: 32 AF XY: 0.649 AC XY: 48185 AN XY: 74286

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.666

Alfa AF: 0.621 Hom.: 3565

Bravo AF: 0.674

Asia WGS AF: 0.473 AC: 1646 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074052; hg19: chr9-136462498; COSMIC: COSV60404857;