rs7901888

chr10-68695733-A-Cchr10-68695733-A-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 0.789 in 152,122 control chromosomes in the GnomAD database, including 47,593 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 0.79 (47593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119943 AN: 152004 Hom.: 47582 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.789 AC: 120001 AN: 152122 Hom.: 47593 Cov.: 32 AF XY: 0.786 AC XY: 58469 AN XY: 74368

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.804

Alfa AF: 0.820 Hom.: 66613

Bravo AF: 0.785

Asia WGS AF: 0.758 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.6
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: rs7901888; hg19: chr10-70455490;