rs9500256

Variant names:

• chr6-57982677-G-A
• rs9500256
• ENST00000641775.1:n.171+20429G>A

Variant summary

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

The ENST00000641775.1(ENSG00000225096):​n.171+20429G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,730 control chromosomes in the GnomAD database, including 15,206 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 (15206 hom., cov: 32)
• Consequence: ENSG00000225096 ENST00000641775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 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
ENSG00000225096	ENST00000641775.1	n.171+20429G>A		intron_variant	Intron 1 of 5
ENSG00000225096	ENST00000641829.1	n.443+11021G>A		intron_variant	Intron 4 of 7
ENSG00000225096	ENST00000666847.1	n.124+20429G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66857 AN: 151614 Hom.: 15190 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.441 AC: 66913 AN: 151730 Hom.: 15206 Cov.: 32 AF XY: 0.447 AC XY: 33161 AN XY: 74164

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.459

Alfa AF: 0.434 Hom.: 17387

Bravo AF: 0.444

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.030
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9500256; hg19: chr6-58308955;