10-62710915-C-T

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, non coding transcript 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: ENST00000649548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649548.1	n.160-24836G>A		intron_variant, non_coding_transcript_variant

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;