rs9312176

Variant names:

• chr4-67334098-T-C
• rs9312176

Variant summary

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

The variant allele was found at a frequency of 0.534 in 152,038 control chromosomes in the GnomAD database, including 22,253 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 0.53 (22253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 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

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81228 AN: 151920 Hom.: 22266 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.534 AC: 81217 AN: 152038 Hom.: 22253 Cov.: 32 AF XY: 0.533 AC XY: 39614 AN XY: 74322

African (AFR) AF: 0.435 AC: 18027 AN: 41456

American (AMR) AF: 0.527 AC: 8041 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1945 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2114 AN: 5174

South Asian (SAS) AF: 0.587 AC: 2830 AN: 4818

European-Finnish (FIN) AF: 0.569 AC: 6006 AN: 10562

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40529 AN: 67970

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.555 Hom.: 8465

Bravo AF: 0.525

Asia WGS AF: 0.447 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.49
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9312176; hg19: chr4-68199816;