rs117982730

Positions:

• chr7-126256694-G-A
• chr7-126256694-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0176 in 152,056 control chromosomes in the GnomAD database, including 39 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 0.018 (39 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0176 (2677/152056) while in subpopulation NFE AF= 0.0257 (1746/67968). AF 95% confidence interval is 0.0247. There are 39 homozygotes in gnomad4. There are 1299 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 39 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0176 AC: 2676 AN: 151938 Hom.: 39 Cov.: 32

Gnomad AFR AF: 0.00329

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00477

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0176 AC: 2677 AN: 152056 Hom.: 39 Cov.: 32 AF XY: 0.0175 AC XY: 1299 AN XY: 74326

Gnomad4 AFR AF: 0.00328

Gnomad4 AMR AF: 0.0115

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.00477

Gnomad4 FIN AF: 0.0406

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0166 Hom.: 7

Bravo AF: 0.0139

Asia WGS AF: 0.00318 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117982730; hg19: chr7-125896748;