rs7341022

Variant names:

• chr5-15014073-G-A
• rs7341022

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 0.249 in 151,984 control chromosomes in the GnomAD database, including 5,623 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 0.25 (5623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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: 0.249 AC: 37786 AN: 151866 Hom.: 5595 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.249 AC: 37868 AN: 151984 Hom.: 5623 Cov.: 32 AF XY: 0.247 AC XY: 18321 AN XY: 74304

African (AFR) AF: 0.416 AC: 17224 AN: 41412

American (AMR) AF: 0.185 AC: 2828 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5178

South Asian (SAS) AF: 0.170 AC: 819 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2121 AN: 10546

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12164 AN: 67968

Other (OTH) AF: 0.261 AC: 553 AN: 2116

Alfa AF: 0.197 Hom.: 2380

Bravo AF: 0.256

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.35
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7341022; hg19: chr5-15014182;