rs224030

chr10-62760375-A-G

Variant summary

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

The ENST00000649548.1(ENSG00000238280):n.159+45354T>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 0.557 in 151,974 control chromosomes in the GnomAD database, including 23,855 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 0.56 (23855 hom., cov: 32)
• Consequence: ENST00000649548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.658 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.159+45354T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84568 AN: 151854 Hom.: 23820 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.557 AC: 84655 AN: 151974 Hom.: 23855 Cov.: 32 AF XY: 0.558 AC XY: 41473 AN XY: 74272

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.540

Alfa AF: 0.565 Hom.: 3031

Bravo AF: 0.546

Asia WGS AF: 0.621 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	13
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224030; hg19: chr10-64520135;