7-50408441-C-T

Variant names:

• chr7-50408441-C-T
• rs12719019

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 0.395 in 151,972 control chromosomes in the GnomAD database, including 12,763 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 0.40 (12763 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 18 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 (NFE) allele frequency at 95% confidence interval = 0.491 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: 0.395 AC: 60042 AN: 151852 Hom.: 12760 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.395 AC: 60052 AN: 151972 Hom.: 12763 Cov.: 32 AF XY: 0.387 AC XY: 28733 AN XY: 74294

African (AFR) AF: 0.258 AC: 10675 AN: 41450

American (AMR) AF: 0.359 AC: 5497 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3468

East Asian (EAS) AF: 0.171 AC: 883 AN: 5176

South Asian (SAS) AF: 0.351 AC: 1688 AN: 4812

European-Finnish (FIN) AF: 0.422 AC: 4448 AN: 10532

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33633 AN: 67928

Other (OTH) AF: 0.417 AC: 881 AN: 2114

Alfa AF: 0.446 Hom.: 30822

Bravo AF: 0.383

Asia WGS AF: 0.322 AC: 1121 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	0.20
DANN	Benign	0.25
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs12719019; hg19: chr7-50476139;