rs2957384

Variant names:

• chr17-53657705-G-A
• rs2957384
• ENST00000650577.1:n.659+182127C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650577.1(ENSG00000285939):​n.659+182127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,078 control chromosomes in the GnomAD database, including 2,607 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 0.18 (2607 hom., cov: 32)
• Consequence: ENSG00000285939 ENST00000650577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

ENSG00000285939 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.253 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
ENSG00000285939	ENST00000650577.1	n.659+182127C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26854 AN: 151962 Hom.: 2585 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.177 AC: 26923 AN: 152078 Hom.: 2607 Cov.: 32 AF XY: 0.177 AC XY: 13172 AN XY: 74352

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.185

Alfa AF: 0.160 Hom.: 357

Bravo AF: 0.180

Asia WGS AF: 0.182 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2957384; hg19: chr17-51735066;