rs7911563

chr10-59448533-G-Cchr10-59448533-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 0.509 in 151,960 control chromosomes in the GnomAD database, including 20,371 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 0.51 (20371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 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: 0.510 AC: 77424 AN: 151842 Hom.: 20381 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.509 AC: 77422 AN: 151960 Hom.: 20371 Cov.: 32 AF XY: 0.505 AC XY: 37520 AN XY: 74268

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.552

Alfa AF: 0.525 Hom.: 2583

Bravo AF: 0.503

Asia WGS AF: 0.490 AC: 1704 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7911563; hg19: chr10-61208291;