rs1917939

Variant names:

• chr7-97087552-C-T
• rs1917939

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 0.24 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.170 AC: 7074 AN: 41496

American (AMR) AF: 0.260 AC: 3977 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2297 AN: 5170

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4824

European-Finnish (FIN) AF: 0.250 AC: 2642 AN: 10554

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17589 AN: 67960

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.252 Hom.: 6211

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1917939; hg19: chr7-96716864;