rs10737627

Variant names:

• chr1-193598845-C-T
• rs10737627
• ENST00000656143.2:n.154-74365C>T

Variant summary

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

The ENST00000656143.2(ENSG00000227240):​n.154-74365C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,754 control chromosomes in the GnomAD database, including 24,671 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 0.57 (24671 hom., cov: 31)
• Consequence: ENSG00000227240 ENST00000656143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 1 publications found

Genes affected

ENSG00000227240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5234+125469C>T		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.2	n.154-74365C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86149 AN: 151636 Hom.: 24652 Cov.: 31

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.568 AC: 86214 AN: 151754 Hom.: 24671 Cov.: 31 AF XY: 0.568 AC XY: 42161 AN XY: 74162

African (AFR) AF: 0.597 AC: 24732 AN: 41398

American (AMR) AF: 0.560 AC: 8535 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1813 AN: 3468

East Asian (EAS) AF: 0.737 AC: 3799 AN: 5156

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4816

European-Finnish (FIN) AF: 0.506 AC: 5324 AN: 10522

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37321 AN: 67852

Other (OTH) AF: 0.573 AC: 1204 AN: 2100

Alfa AF: 0.564 Hom.: 8961

Bravo AF: 0.572

Asia WGS AF: 0.653 AC: 2269 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs10737627; hg19: chr1-193567975; COSMIC: COSV50951425;