rs9313296

Variant names:

• chr5-165950694-G-C
• rs9313296

Your query was ambiguous. Multiple possible variants found:

• chr5-165950694-G-C
• chr5-165950694-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 0.123 in 152,094 control chromosomes in the GnomAD database, including 3,013 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 0.12 (3013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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 = 0.366 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: 0.123 AC: 18653 AN: 151976 Hom.: 2995 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0635

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.00715

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00697

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.123 AC: 18711 AN: 152094 Hom.: 3013 Cov.: 32 AF XY: 0.119 AC XY: 8840 AN XY: 74360

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.00716

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.00697

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0298 Hom.: 129

Bravo AF: 0.141

Asia WGS AF: 0.0480 AC: 166 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
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: rs9313296; hg19: chr5-165377699;