rs1357949

Variant names:

• chr7-122993210-A-G
• rs1357949

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 0.255 in 152,044 control chromosomes in the GnomAD database, including 5,594 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 (5594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38680 AN: 151926 Hom.: 5585 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.255 AC: 38698 AN: 152044 Hom.: 5594 Cov.: 32 AF XY: 0.256 AC XY: 19039 AN XY: 74294

African (AFR) AF: 0.136 AC: 5630 AN: 41504

American (AMR) AF: 0.397 AC: 6051 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1205 AN: 3466

East Asian (EAS) AF: 0.161 AC: 830 AN: 5140

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4820

European-Finnish (FIN) AF: 0.243 AC: 2569 AN: 10582

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20484 AN: 67962

Other (OTH) AF: 0.283 AC: 598 AN: 2110

Alfa AF: 0.202 Hom.: 672

Bravo AF: 0.264

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.78
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs1357949; hg19: chr7-122633264;