rs6460751

Variant names:

• chr7-10805476-T-C
• rs6460751

Your query was ambiguous. Multiple possible variants found:

• chr7-10805476-T-C
• chr7-10805476-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.382 AC: 15855 AN: 41492

American (AMR) AF: 0.195 AC: 2975 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1135 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1962 AN: 5180

South Asian (SAS) AF: 0.209 AC: 1010 AN: 4828

European-Finnish (FIN) AF: 0.281 AC: 2977 AN: 10578

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18446 AN: 67990

Other (OTH) AF: 0.272 AC: 575 AN: 2114

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
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs6460751; hg19: chr7-10845103;