rs956312

Variant names:

• chr4-10186702-G-A
• rs956312

Your query was ambiguous. Multiple possible variants found:

• chr4-10186702-G-A
• chr4-10186702-G-C
• chr4-10186702-G-T

Variant summary

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

The variant allele was found at a frequency of 0.601 in 152,034 control chromosomes in the GnomAD database, including 28,330 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 0.60 (28330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 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: 0.601 AC: 91243 AN: 151916 Hom.: 28309 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.601 AC: 91301 AN: 152034 Hom.: 28330 Cov.: 32 AF XY: 0.602 AC XY: 44727 AN XY: 74296

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.596

Alfa AF: 0.664 Hom.: 67277

Bravo AF: 0.582

Asia WGS AF: 0.619 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs956312; hg19: chr4-10188326;