rs10485968

chr7-81834070-G-C

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 0.145 in 151,996 control chromosomes in the GnomAD database, including 1,954 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 0.14 (1954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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: 0.145 AC: 21989 AN: 151878 Hom.: 1956 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0583

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.145 AC: 21987 AN: 151996 Hom.: 1954 Cov.: 32 AF XY: 0.142 AC XY: 10564 AN XY: 74278

Gnomad4 AFR AF: 0.0693

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0587

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.137

Alfa AF: 0.175 Hom.: 319

Bravo AF: 0.136

Asia WGS AF: 0.0940 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.49
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485968; hg19: chr7-81463386;