chr17-64937405-G-A

Variant names:

• chr17-64937405-G-A
• rs2221741
• ENST00000577423.3:n.321-3178G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577423.3(ENSG00000290457):​n.321-3178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,164 control chromosomes in the GnomAD database, including 3,907 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 0.12 (3907 hom., cov: 32)
• Consequence: ENSG00000290457 ENST00000577423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 0 publications found

Genes affected

ENSG00000290457 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577423.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290457	ENST00000577423.3	TSL:3	n.321-3178G>A		intron	N/A
	ENSG00000266155	ENST00000578601.2	TSL:6	n.63-726C>T		intron	N/A
	ENSG00000290457	ENST00000717272.1		n.218+158G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18632 AN: 152046 Hom.: 3886 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00106

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.123 AC: 18701 AN: 152164 Hom.: 3907 Cov.: 32 AF XY: 0.119 AC XY: 8890 AN XY: 74410

African (AFR) AF: 0.429 AC: 17754 AN: 41430

American (AMR) AF: 0.0436 AC: 667 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4830

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00106 AC: 72 AN: 68020

Other (OTH) AF: 0.0878 AC: 185 AN: 2108

Alfa AF: 0.0817 Hom.: 731

Bravo AF: 0.140

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2221741; hg19: chr17-62933523;