7-127432641-T-G

Variant names:

• chr7-127432641-T-G
• rs2106177

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 0.321 in 152,062 control chromosomes in the GnomAD database, including 10,147 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 0.32 (10147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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: 0.321 AC: 48731 AN: 151944 Hom.: 10135 Cov.: 32

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.321 AC: 48749 AN: 152062 Hom.: 10147 Cov.: 32 AF XY: 0.331 AC XY: 24600 AN XY: 74324

African (AFR) AF: 0.0790 AC: 3281 AN: 41526

American (AMR) AF: 0.389 AC: 5945 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3472

East Asian (EAS) AF: 0.801 AC: 4144 AN: 5172

South Asian (SAS) AF: 0.490 AC: 2362 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4726 AN: 10534

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26391 AN: 67942

Other (OTH) AF: 0.319 AC: 674 AN: 2114

Alfa AF: 0.241 Hom.: 707

Bravo AF: 0.308

Asia WGS AF: 0.568 AC: 1969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs2106177; hg19: chr7-127072695;