7-127433905-T-C

Variant names:

• chr7-127433905-T-C
• rs10487482

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 152,018 control chromosomes in the GnomAD database, including 10,157 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 (10157 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 48789 AN: 151900 Hom.: 10145 Cov.: 31

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.389

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: 48808 AN: 152018 Hom.: 10157 Cov.: 31 AF XY: 0.331 AC XY: 24592 AN XY: 74268

African (AFR) AF: 0.0800 AC: 3322 AN: 41512

American (AMR) AF: 0.389 AC: 5946 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3468

East Asian (EAS) AF: 0.801 AC: 4150 AN: 5182

South Asian (SAS) AF: 0.490 AC: 2358 AN: 4810

European-Finnish (FIN) AF: 0.447 AC: 4706 AN: 10520

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26430 AN: 67936

Other (OTH) AF: 0.319 AC: 672 AN: 2106

Alfa AF: 0.358 Hom.: 1799

Bravo AF: 0.308

Asia WGS AF: 0.568 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
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: rs10487482; hg19: chr7-127073959;