chr17-38620728-G-T

Variant names:

• chr17-38620728-G-T
• rs2075052

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 0.104 in 152,234 control chromosomes in the GnomAD database, including 1,439 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 0.10 (1439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 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: 0.104 AC: 15793 AN: 152116 Hom.: 1434 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.104 AC: 15802 AN: 152234 Hom.: 1439 Cov.: 32 AF XY: 0.110 AC XY: 8208 AN XY: 74422

African (AFR) AF: 0.0255 AC: 1062 AN: 41576

American (AMR) AF: 0.144 AC: 2203 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2581 AN: 5150

South Asian (SAS) AF: 0.113 AC: 546 AN: 4822

European-Finnish (FIN) AF: 0.144 AC: 1531 AN: 10596

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7183 AN: 68016

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.106 Hom.: 2794

Bravo AF: 0.104

Asia WGS AF: 0.295 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.93
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs2075052; hg19: chr17-36776981;