rs10737627

chr1-193598845-C-T

Variant summary

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

The ENST00000656143.1(ENSG00000227240):n.154-74365C>T variant causes a intron, non coding transcript 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: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124904475	XR_007066777.1	n.5234+125469C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656143.1	n.154-74365C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.573

Alfa AF: 0.555 Hom.: 4629

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

Splicing

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

Publications

LitVar

Other links and lift over

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