rs1917939

Positions:

• chr7-97087552-C-T

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 0.24 in 152,064 control chromosomes in the GnomAD database, including 4,638 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 0.24 (4638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

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: 0.240 AC: 36514 AN: 151946 Hom.: 4638 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.240 AC: 36525 AN: 152064 Hom.: 4638 Cov.: 32 AF XY: 0.241 AC XY: 17878 AN XY: 74312

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.270

Alfa AF: 0.254 Hom.: 5051

Bravo AF: 0.239

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1917939; hg19: chr7-96716864;