chr7-106851232-A-G

Variant names:

• chr7-106851232-A-G
• rs1724262

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 0.655 in 152,084 control chromosomes in the GnomAD database, including 33,100 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 0.65 (33100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.655 AC: 99510 AN: 151966 Hom.: 33060 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.655 AC: 99611 AN: 152084 Hom.: 33100 Cov.: 32 AF XY: 0.657 AC XY: 48864 AN XY: 74326

African (AFR) AF: 0.711 AC: 29486 AN: 41470

American (AMR) AF: 0.608 AC: 9298 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2292 AN: 3468

East Asian (EAS) AF: 0.963 AC: 4985 AN: 5178

South Asian (SAS) AF: 0.670 AC: 3234 AN: 4828

European-Finnish (FIN) AF: 0.652 AC: 6894 AN: 10566

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41401 AN: 67976

Other (OTH) AF: 0.657 AC: 1386 AN: 2108

Alfa AF: 0.625 Hom.: 16509

Bravo AF: 0.652

Asia WGS AF: 0.801 AC: 2785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.078
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1724262; hg19: chr7-106491677;