rs17749368

Variant names:

• chr7-63101106-T-C
• rs17749368

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 0.134 in 152,082 control chromosomes in the GnomAD database, including 1,659 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 0.13 (1659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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: 0.134 AC: 20357 AN: 151964 Hom.: 1657 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.134 AC: 20355 AN: 152082 Hom.: 1659 Cov.: 32 AF XY: 0.131 AC XY: 9710 AN XY: 74352

African (AFR) AF: 0.0387 AC: 1606 AN: 41498

American (AMR) AF: 0.139 AC: 2117 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3468

East Asian (EAS) AF: 0.104 AC: 537 AN: 5140

South Asian (SAS) AF: 0.123 AC: 591 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1494 AN: 10592

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12956 AN: 67982

Other (OTH) AF: 0.142 AC: 300 AN: 2108

Alfa AF: 0.162 Hom.: 428

Bravo AF: 0.130

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs17749368; hg19: chr7-62561484;