rs6460751

chr7-10805476-T-Cchr7-10805476-T-G

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 0.297 in 152,134 control chromosomes in the GnomAD database, including 7,070 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 (7070 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.298 AC: 45232 AN: 152016 Hom.: 7064 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.297 AC: 45259 AN: 152134 Hom.: 7070 Cov.: 33 AF XY: 0.298 AC XY: 22129 AN XY: 74378

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.272

Alfa AF: 0.179 Hom.: 486

Bravo AF: 0.296

Asia WGS AF: 0.278 AC: 966 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6460751; hg19: chr7-10845103;