rs1357949

Positions:

• chr7-122993210-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.283

Alfa AF: 0.204 Hom.: 664

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1357949; hg19: chr7-122633264;