rs3895874

Positions:

• chr17-48970506-G-A
• chr17-48970506-G-C
• chr17-48970506-G-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 0.46 in 152,044 control chromosomes in the GnomAD database, including 17,746 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 0.46 (17746 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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: 0.460 AC: 69871 AN: 151926 Hom.: 17753 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.460 AC: 69871 AN: 152044 Hom.: 17746 Cov.: 33 AF XY: 0.460 AC XY: 34214 AN XY: 74326

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.482

Alfa AF: 0.540 Hom.: 28263

Bravo AF: 0.445

Asia WGS AF: 0.563 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.056
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3895874; hg19: chr17-47047868;