17-48968914-A-G

Variant names:

• chr17-48968914-A-G
• rs937301

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 0.542 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.542 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

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.519

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs937301; hg19: chr17-47046276;