rs6945381

Variant names:

• chr7-12259656-C-A
• rs6945381

Your query was ambiguous. Multiple possible variants found:

• chr7-12259656-C-A
• chr7-12259656-C-T

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 0.119 in 152,150 control chromosomes in the GnomAD database, including 2,605 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 0.12 (2605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.119 AC: 18117 AN: 152034 Hom.: 2602 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0445

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.119 AC: 18151 AN: 152150 Hom.: 2605 Cov.: 32 AF XY: 0.118 AC XY: 8774 AN XY: 74376

African (AFR) AF: 0.336 AC: 13923 AN: 41448

American (AMR) AF: 0.0444 AC: 679 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.155 AC: 802 AN: 5180

South Asian (SAS) AF: 0.174 AC: 838 AN: 4824

European-Finnish (FIN) AF: 0.0136 AC: 144 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1309 AN: 68014

Other (OTH) AF: 0.109 AC: 230 AN: 2110

Alfa AF: 0.0103 Hom.: 14

Bravo AF: 0.130

Asia WGS AF: 0.195 AC: 675 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	6.2
DANN	Benign	0.22
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs6945381; hg19: chr7-12299282;