chr10-62760375-A-G

Variant names:

• chr10-62760375-A-G
• rs224030
• ENST00000649548.2:n.159+45354T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649548.2(ENSG00000238280):​n.159+45354T>C variant causes a intron 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: ENSG00000238280 ENST00000649548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877
• Publications: 5 publications found

Genes affected

ENSG00000238280 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000238280	ENST00000649548.2	n.159+45354T>C		intron_variant	Intron 1 of 3
ENSG00000238280	ENST00000821260.1	n.165-31304T>C		intron_variant	Intron 1 of 1
ENSG00000238280	ENST00000821261.1	n.426-31304T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.517 AC: 21421 AN: 41426

American (AMR) AF: 0.540 AC: 8260 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3466

East Asian (EAS) AF: 0.484 AC: 2498 AN: 5164

South Asian (SAS) AF: 0.678 AC: 3266 AN: 4818

European-Finnish (FIN) AF: 0.568 AC: 5992 AN: 10542

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39673 AN: 67960

Other (OTH) AF: 0.540 AC: 1138 AN: 2108

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
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs224030; hg19: chr10-64520135;