rs2421031

chr10-122662592-T-C

Variant summary

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

The ENST00000652317.1(ENSG00000286114):n.47-1441T>C 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 0.347 in 151,788 control chromosomes in the GnomAD database, including 10,886 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 0.35 (10886 hom., cov: 31)
• Consequence: ENST00000652317.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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
	ENST00000652317.1	n.47-1441T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52583 AN: 151670 Hom.: 10872 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.347 AC: 52627 AN: 151788 Hom.: 10886 Cov.: 31 AF XY: 0.344 AC XY: 25476 AN XY: 74162

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.316

Alfa AF: 0.309 Hom.: 1050

Bravo AF: 0.362

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.32
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421031; hg19: chr10-124422108;