chr7-127285907-C-T

Variant names:

• chr7-127285907-C-T
• rs975308

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 0.574 in 151,892 control chromosomes in the GnomAD database, including 28,012 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 0.57 (28012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87067 AN: 151774 Hom.: 27971 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.574 AC: 87147 AN: 151892 Hom.: 28012 Cov.: 32 AF XY: 0.562 AC XY: 41701 AN XY: 74214

African (AFR) AF: 0.864 AC: 35863 AN: 41492

American (AMR) AF: 0.480 AC: 7330 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2363 AN: 3470

East Asian (EAS) AF: 0.166 AC: 855 AN: 5146

South Asian (SAS) AF: 0.376 AC: 1804 AN: 4804

European-Finnish (FIN) AF: 0.393 AC: 4115 AN: 10472

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32876 AN: 67922

Other (OTH) AF: 0.578 AC: 1221 AN: 2112

Alfa AF: 0.533 Hom.: 2904

Bravo AF: 0.594

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs975308; hg19: chr7-126925961;