chr7-106862953-A-G

Variant names:

• chr7-106862953-A-G
• rs12705393

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 0.191 in 152,218 control chromosomes in the GnomAD database, including 3,533 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 0.19 (3533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.191 AC: 29125 AN: 152100 Hom.: 3533 Cov.: 33

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.191 AC: 29131 AN: 152218 Hom.: 3533 Cov.: 33 AF XY: 0.192 AC XY: 14263 AN XY: 74428

African (AFR) AF: 0.0505 AC: 2100 AN: 41562

American (AMR) AF: 0.223 AC: 3405 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3472

East Asian (EAS) AF: 0.00983 AC: 51 AN: 5188

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4824

European-Finnish (FIN) AF: 0.272 AC: 2881 AN: 10582

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18188 AN: 67982

Other (OTH) AF: 0.194 AC: 408 AN: 2108

Alfa AF: 0.223 Hom.: 6806

Bravo AF: 0.182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.41
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs12705393; hg19: chr7-106503398;