rs1227244

Variant names:

• chr10-64831068-A-G
• rs1227244
• ENST00000718642.1:n.195+16066A>G

Variant summary

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

The ENST00000718642.1(ENSG00000293732):​n.195+16066A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,694 control chromosomes in the GnomAD database, including 9,823 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 0.36 (9823 hom., cov: 32)
• Consequence: ENSG00000293732 ENST00000718642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 4 publications found

Genes affected

ENSG00000293732 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378336	XR_946020.2	n.49+16066A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293732	ENST00000718642.1	n.195+16066A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53971 AN: 151576 Hom.: 9810 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.356 AC: 54013 AN: 151694 Hom.: 9823 Cov.: 32 AF XY: 0.357 AC XY: 26460 AN XY: 74144

African (AFR) AF: 0.440 AC: 18205 AN: 41354

American (AMR) AF: 0.246 AC: 3734 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3466

East Asian (EAS) AF: 0.276 AC: 1421 AN: 5152

South Asian (SAS) AF: 0.357 AC: 1720 AN: 4818

European-Finnish (FIN) AF: 0.395 AC: 4153 AN: 10512

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22736 AN: 67884

Other (OTH) AF: 0.350 AC: 737 AN: 2108

Alfa AF: 0.343 Hom.: 2104

Bravo AF: 0.347

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.0
DANN	Benign	0.62
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1227244; hg19: chr10-66590825;