rs10513025

Variant names:

• chr5-9623510-T-C
• rs10513025
• ENST00000504182.2:n.128A>G

Variant summary

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

The ENST00000504182.2(ENSG00000248525):​n.128A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 152,472 control chromosomes in the GnomAD database, including 315 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 0.053 (315 hom., cov: 32)
  • Exomes 𝑓: 0.031 (0 hom.)
• Consequence: ENSG00000248525 ENST00000504182.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 30 publications found

Genes affected

ENSG00000248525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 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
ENSG00000248525	ENST00000504182.2	n.128A>G		non_coding_transcript_exon_variant	Exon 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8075 AN: 152162 Hom.: 312 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0559

GnomAD4 exome AF: 0.0313 AC: 6 AN: 192 Hom.: 0 Cov.: 0 AF XY: 0.0273 AC XY: 3 AN XY: 110

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 18

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0417 AC: 1 AN: 24

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0294 AC: 4 AN: 136

Other (OTH) AF: 0.125 AC: 1 AN: 8

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00969391), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0532 AC: 8094 AN: 152280 Hom.: 315 Cov.: 32 AF XY: 0.0520 AC XY: 3868 AN XY: 74452

African (AFR) AF: 0.107 AC: 4456 AN: 41542

American (AMR) AF: 0.0323 AC: 495 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4822

European-Finnish (FIN) AF: 0.0265 AC: 281 AN: 10622

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2329 AN: 68016

Other (OTH) AF: 0.0558 AC: 118 AN: 2114

Alfa AF: 0.0398 Hom.: 490

Bravo AF: 0.0565

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.73
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10513025; hg19: chr5-9623622;