chr7-48953756-T-C

Variant names:

• chr7-48953756-T-C
• rs763873

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 0.116 in 152,174 control chromosomes in the GnomAD database, including 1,522 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 0.12 (1522 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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: 0.116 AC: 17615 AN: 152058 Hom.: 1516 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.116 AC: 17651 AN: 152174 Hom.: 1522 Cov.: 33 AF XY: 0.114 AC XY: 8444 AN XY: 74386

African (AFR) AF: 0.247 AC: 10233 AN: 41466

American (AMR) AF: 0.0751 AC: 1150 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.0667 AC: 345 AN: 5172

South Asian (SAS) AF: 0.159 AC: 766 AN: 4812

European-Finnish (FIN) AF: 0.0436 AC: 463 AN: 10618

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4277 AN: 68016

Other (OTH) AF: 0.104 AC: 219 AN: 2110

Alfa AF: 0.0982 Hom.: 305

Bravo AF: 0.123

Asia WGS AF: 0.131 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs763873; hg19: chr7-48993352;