1-193598845-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656143.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227240	ENST00000656143.2		n.154-74365C>T		intron	N/A

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 v4.9

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;