17-48968914-A-G

Variant names:

• chr17-48968914-A-G
• rs937301

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 0.542 in 152,006 control chromosomes in the GnomAD database, including 23,992 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 0.54 (23992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82294 AN: 151888 Hom.: 23943 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.542 AC: 82408 AN: 152006 Hom.: 23992 Cov.: 32 AF XY: 0.540 AC XY: 40155 AN XY: 74298

African (AFR) AF: 0.765 AC: 31721 AN: 41466

American (AMR) AF: 0.544 AC: 8283 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1578 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1502 AN: 5150

South Asian (SAS) AF: 0.464 AC: 2236 AN: 4818

European-Finnish (FIN) AF: 0.460 AC: 4857 AN: 10562

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30655 AN: 67984

Other (OTH) AF: 0.519 AC: 1097 AN: 2114

Alfa AF: 0.512 Hom.: 3383

Bravo AF: 0.555

Asia WGS AF: 0.432 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.18
PromoterAI		-0.026	Neutral

Splicing

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

Other links and lift over

dbSNP: rs937301; hg19: chr17-47046276;