rs9312202

Variant names:

• chr4-176973111-G-C
• rs9312202
• ENST00000656694.1:n.347-79206C>G

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.347-79206C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,074 control chromosomes in the GnomAD database, including 2,653 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 (2653 hom., cov: 32)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287544	ENST00000656694.1	n.347-79206C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17158 AN: 151956 Hom.: 2641 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00628

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.113 AC: 17211 AN: 152074 Hom.: 2653 Cov.: 32 AF XY: 0.112 AC XY: 8311 AN XY: 74350

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0816

Gnomad4 SAS AF: 0.0645

Gnomad4 FIN AF: 0.0359

Gnomad4 NFE AF: 0.00628

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.0659 Hom.: 178

Bravo AF: 0.127

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9312202; hg19: chr4-177894265;