chr17-48968914-A-G

Position:

• chr17-48968914-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;