7-126320989-C-T

Variant names:

• chr7-126320989-C-T
• rs485

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 0.338 in 151,736 control chromosomes in the GnomAD database, including 9,493 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 0.34 (9493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51342 AN: 151618 Hom.: 9500 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.338 AC: 51355 AN: 151736 Hom.: 9493 Cov.: 32 AF XY: 0.336 AC XY: 24927 AN XY: 74132

African (AFR) AF: 0.186 AC: 7700 AN: 41440

American (AMR) AF: 0.389 AC: 5928 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1797 AN: 3452

East Asian (EAS) AF: 0.398 AC: 2052 AN: 5156

South Asian (SAS) AF: 0.440 AC: 2126 AN: 4828

European-Finnish (FIN) AF: 0.298 AC: 3128 AN: 10512

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27453 AN: 67812

Other (OTH) AF: 0.380 AC: 800 AN: 2104

Alfa AF: 0.392 Hom.: 43820

Bravo AF: 0.334

Asia WGS AF: 0.404 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.42
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs485; hg19: chr7-125961043;