rs224123

Positions:

• chr10-62691473-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000649548.1(ENSG00000238280):​n.160-5394G>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 0.679 in 152,132 control chromosomes in the GnomAD database, including 37,019 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 0.68 (37019 hom., cov: 32)
• Consequence: ENST00000649548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649548.1	n.160-5394G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103156 AN: 152014 Hom.: 36949 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.679 AC: 103288 AN: 152132 Hom.: 37019 Cov.: 32 AF XY: 0.675 AC XY: 50213 AN XY: 74362

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.643

Alfa AF: 0.615 Hom.: 6823

Bravo AF: 0.685

Asia WGS AF: 0.640 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224123; hg19: chr10-64451233;