7-153574792-C-T

Variant names:

• chr7-153574792-C-T
• rs11771429

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 0.14 in 152,200 control chromosomes in the GnomAD database, including 1,934 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 0.14 (1934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.28 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: 0.140 AC: 21342 AN: 152080 Hom.: 1934 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.140 AC: 21351 AN: 152200 Hom.: 1934 Cov.: 32 AF XY: 0.145 AC XY: 10767 AN XY: 74394

African (AFR) AF: 0.0330 AC: 1371 AN: 41548

American (AMR) AF: 0.195 AC: 2977 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1511 AN: 5172

South Asian (SAS) AF: 0.179 AC: 861 AN: 4820

European-Finnish (FIN) AF: 0.179 AC: 1891 AN: 10582

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11373 AN: 67990

Other (OTH) AF: 0.145 AC: 306 AN: 2116

Alfa AF: 0.158 Hom.: 3498

Bravo AF: 0.137

Asia WGS AF: 0.231 AC: 805 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	4.6
DANN	Benign	0.76
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11771429; hg19: chr7-153271877;