5-111091630-C-T

Variant names:

• chr5-111091630-C-T
• rs10050834
• ENST00000507269.3:n.46+440G>A

Variant summary

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

The ENST00000507269.3(ENSG00000253613):​n.46+440G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,536 control chromosomes in the GnomAD database, including 21,586 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 0.52 (21533 hom., cov: 32)
  • Exomes 𝑓: 0.41 (53 hom.)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 7 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 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
ENSG00000253613	ENST00000507269.3	n.46+440G>A		intron_variant	Intron 1 of 3	5
ENSG00000253613	ENST00000741219.1	n.136+440G>A		intron_variant	Intron 1 of 2
ENSG00000253613	ENST00000741220.1	n.136+440G>A		intron_variant	Intron 1 of 1
ENSG00000253613	ENST00000741221.1	n.99+424G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79437 AN: 151924 Hom.: 21511 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.504

GnomAD4 exome AF: 0.412 AC: 202 AN: 490 Hom.: 53 AF XY: 0.438 AC XY: 114 AN XY: 260

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.517 AC: 31 AN: 60

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.636 AC: 14 AN: 22

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.383 AC: 147 AN: 384

Other (OTH) AF: 0.357 AC: 5 AN: 14

GnomAD4 genome AF: 0.523 AC: 79515 AN: 152046 Hom.: 21533 Cov.: 32 AF XY: 0.528 AC XY: 39248 AN XY: 74318

African (AFR) AF: 0.648 AC: 26864 AN: 41474

American (AMR) AF: 0.510 AC: 7794 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1675 AN: 5162

South Asian (SAS) AF: 0.673 AC: 3238 AN: 4814

European-Finnish (FIN) AF: 0.546 AC: 5777 AN: 10578

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30957 AN: 67952

Other (OTH) AF: 0.502 AC: 1062 AN: 2114

Alfa AF: 0.504 Hom.: 2537

Bravo AF: 0.518

Asia WGS AF: 0.497 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.51
DANN	Benign	0.85
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10050834; hg19: chr5-110427328;