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. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.310 AC: 12850 AN: 41480

American (AMR) AF: 0.199 AC: 3048 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1692 AN: 5164

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4820

European-Finnish (FIN) AF: 0.365 AC: 3855 AN: 10564

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20835 AN: 67990

Other (OTH) AF: 0.261 AC: 550 AN: 2106

Alfa AF: 0.289 Hom.: 18323

Bravo AF: 0.285

Asia WGS AF: 0.302 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	19
DANN	Benign	0.51
PhyloP100		1.7

Splicing

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

Other links and lift over

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