rs1010376

Variant names:

• chr5-72007481-G-A
• rs1010376

Your query was ambiguous. Multiple possible variants found:

• chr5-72007481-G-A
• chr5-72007481-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.299 in 152,084 control chromosomes in the GnomAD database, including 6,987 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 0.30 (6987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 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: 0.299 AC: 45480 AN: 151966 Hom.: 6982 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.299 AC: 45503 AN: 152084 Hom.: 6987 Cov.: 32 AF XY: 0.300 AC XY: 22291 AN XY: 74338

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.261

Alfa AF: 0.286 Hom.: 10882

Bravo AF: 0.285

Asia WGS AF: 0.302 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	19
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1010376; hg19: chr5-71303308; COSMIC: COSV60153861;