ENST00000649548.2:n.160-31997C>T

Variant names:

• chr10-62718076-G-A
• rs224143
• ENST00000649548.2:n.160-31997C>T

Variant summary

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

The ENST00000649548.2(ENSG00000238280):​n.160-31997C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,990 control chromosomes in the GnomAD database, including 31,337 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 0.63 (31337 hom., cov: 31)
• Consequence: ENSG00000238280 ENST00000649548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000238280	ENST00000649548.2		n.160-31997C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96258 AN: 151872 Hom.: 31283 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.634 AC: 96372 AN: 151990 Hom.: 31337 Cov.: 31 AF XY: 0.632 AC XY: 46945 AN XY: 74256

African (AFR) AF: 0.778 AC: 32247 AN: 41466

American (AMR) AF: 0.573 AC: 8754 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2272 AN: 5166

South Asian (SAS) AF: 0.683 AC: 3296 AN: 4826

European-Finnish (FIN) AF: 0.564 AC: 5940 AN: 10530

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40031 AN: 67950

Other (OTH) AF: 0.608 AC: 1282 AN: 2108

Alfa AF: 0.620 Hom.: 3847

Bravo AF: 0.635

Asia WGS AF: 0.630 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.91
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs224143; hg19: chr10-64477836;