17-49958675-T-A

Variant names:

• chr17-49958675-T-A
• rs12453270

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 0.443 in 151,784 control chromosomes in the GnomAD database, including 18,158 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 0.44 (18158 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.64 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: 0.443 AC: 67193 AN: 151666 Hom.: 18151 Cov.: 29

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.443 AC: 67205 AN: 151784 Hom.: 18158 Cov.: 29 AF XY: 0.444 AC XY: 32934 AN XY: 74148

African (AFR) AF: 0.115 AC: 4770 AN: 41408

American (AMR) AF: 0.582 AC: 8877 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1736 AN: 3466

East Asian (EAS) AF: 0.658 AC: 3375 AN: 5126

South Asian (SAS) AF: 0.430 AC: 2065 AN: 4798

European-Finnish (FIN) AF: 0.584 AC: 6133 AN: 10504

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38677 AN: 67918

Other (OTH) AF: 0.487 AC: 1025 AN: 2104

Alfa AF: 0.488 Hom.: 2475

Bravo AF: 0.431

Asia WGS AF: 0.516 AC: 1793 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	8.6
DANN	Benign	0.78
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs12453270; hg19: chr17-48036039;