rs10457526

Variant names:

• chr6-129575356-G-T
• rs10457526
• ENST00000657779.1:n.48+20C>A

Variant summary

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

The ENST00000657779.1(ENSG00000226149):​n.48+20C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,992 control chromosomes in the GnomAD database, including 3,960 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 0.22 (3960 hom., cov: 31)
• Consequence: ENSG00000226149 ENST00000657779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

ENSG00000226149 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.327 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
ENSG00000226149	ENST00000657779.1	n.48+20C>A		intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000665046.1	n.30+662C>A		intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000670413.1	n.48+20C>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33551 AN: 151874 Hom.: 3954 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.221 AC: 33568 AN: 151992 Hom.: 3960 Cov.: 31 AF XY: 0.226 AC XY: 16788 AN XY: 74292

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.203

Alfa AF: 0.209 Hom.: 7314

Bravo AF: 0.226

Asia WGS AF: 0.267 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10457526; hg19: chr6-129896501;