rs7071471

Variant names:

• chr10-46092487-G-A
• rs7071471

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 0.473 in 152,008 control chromosomes in the GnomAD database, including 17,230 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 0.47 (17230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 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: 0.473 AC: 71778 AN: 151890 Hom.: 17196 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.473 AC: 71867 AN: 152008 Hom.: 17230 Cov.: 32 AF XY: 0.474 AC XY: 35239 AN XY: 74302

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.486

Alfa AF: 0.462 Hom.: 14088

Bravo AF: 0.472

Asia WGS AF: 0.512 AC: 1779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071471; hg19: chr10-51503335;