10-62685804-A-G

Variant names:

• chr10-62685804-A-G
• rs10761659
• ENST00000649548.2:n.199+236T>C

Variant summary

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

The ENST00000649548.2(ENSG00000238280):​n.199+236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,152 control chromosomes in the GnomAD database, including 17,602 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 0.44 (17602 hom., cov: 32)
• Consequence: ENSG00000238280 ENST00000649548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 103 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649548.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000238280	ENST00000649548.2		n.199+236T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66642 AN: 152034 Hom.: 17594 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.438 AC: 66646 AN: 152152 Hom.: 17602 Cov.: 32 AF XY: 0.444 AC XY: 33053 AN XY: 74394

African (AFR) AF: 0.136 AC: 5645 AN: 41534

American (AMR) AF: 0.543 AC: 8299 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3466

East Asian (EAS) AF: 0.762 AC: 3945 AN: 5178

South Asian (SAS) AF: 0.640 AC: 3093 AN: 4832

European-Finnish (FIN) AF: 0.516 AC: 5459 AN: 10572

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36774 AN: 67974

Other (OTH) AF: 0.439 AC: 928 AN: 2114

Alfa AF: 0.513 Hom.: 79302

Bravo AF: 0.424

Asia WGS AF: 0.607 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		0.60

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10761659;

hg19: chr10-64445564;