rs10514635

Variant names:

• chr2-16730399-G-A
• rs10514635
• ENST00000423925.6:n.59+2220G>A

Variant summary

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

The ENST00000423925.6(ENSG00000223536):​n.59+2220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 148,402 control chromosomes in the GnomAD database, including 303 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 (303 hom., cov: 32)
• Consequence: ENSG00000223536 ENST00000423925.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

Genes affected

ENSG00000223536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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
ENSG00000223536	ENST00000423925.6	n.59+2220G>A		intron_variant	Intron 1 of 2	4
ENSG00000223536	ENST00000448650.1	n.56+2220G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 7872 AN: 148310 Hom.: 301 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0323

Gnomad ASJ AF: 0.0439

Gnomad EAS AF: 0.00913

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0877

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0519

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

GnomAD4 genome AF: 0.0531 AC: 7887 AN: 148402 Hom.: 303 Cov.: 32 AF XY: 0.0523 AC XY: 3794 AN XY: 72522

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0439

Gnomad4 EAS AF: 0.00915

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0331

Gnomad4 OTH AF: 0.0514

Alfa AF: 0.0519 Hom.: 26

Bravo AF: 0.0537

Asia WGS AF: 0.0390 AC: 137 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514635; hg19: chr2-16911666;