chr7-19167400-C-T

Variant names:

• chr7-19167400-C-T
• rs17140788

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 0.121 in 152,014 control chromosomes in the GnomAD database, including 1,848 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 (1848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.121 AC: 18311 AN: 151896 Hom.: 1835 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.0849

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.121 AC: 18361 AN: 152014 Hom.: 1848 Cov.: 32 AF XY: 0.121 AC XY: 9018 AN XY: 74320

African (AFR) AF: 0.267 AC: 11075 AN: 41458

American (AMR) AF: 0.0829 AC: 1264 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0849 AC: 294 AN: 3464

East Asian (EAS) AF: 0.129 AC: 664 AN: 5152

South Asian (SAS) AF: 0.0686 AC: 331 AN: 4828

European-Finnish (FIN) AF: 0.0715 AC: 757 AN: 10592

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0526 AC: 3575 AN: 67952

Other (OTH) AF: 0.0848 AC: 179 AN: 2110

Alfa AF: 0.0402 Hom.: 54

Bravo AF: 0.128

Asia WGS AF: 0.120 AC: 414 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.46
DANN	Benign	0.45
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs17140788; hg19: chr7-19207023;