chr10-62710915-C-T

Variant names:

• chr10-62710915-C-T
• rs224136
• ENST00000649548.1:n.160-24836G>A

Variant summary

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

The ENST00000649548.1(ENSG00000238280):​n.160-24836G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,060 control chromosomes in the GnomAD database, including 12,954 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 0.34 (12954 hom., cov: 32)
• Consequence: ENSG00000238280 ENST00000649548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

ENSG00000238280 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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
ENSG00000238280	ENST00000649548.1	n.160-24836G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50861 AN: 151942 Hom.: 12905 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.335 AC: 50972 AN: 152060 Hom.: 12954 Cov.: 32 AF XY: 0.334 AC XY: 24861 AN XY: 74346

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.316

Alfa AF: 0.178 Hom.: 5521

Bravo AF: 0.355

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.8
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: rs224136; hg19: chr10-64470675;