rs224143

Variant names:

• chr10-62718076-G-A
• rs224143
• ENST00000649548.1:n.160-31997C>T

Variant summary

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

The ENST00000649548.1(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 ENST00000649548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

ENSG00000238280 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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	ENST00000649548.1	n.160-31997C>T		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.608

Alfa AF: 0.614 Hom.: 3614

Bravo AF: 0.635

Asia WGS AF: 0.630 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224143; hg19: chr10-64477836;