rs12140698

Variant names:

• chr1-177477780-C-T
• rs12140698
• ENST00000438575.7:n.389-83992G>A

Variant summary

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

The ENST00000438575.7(ENSG00000227579):​n.389-83992G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,114 control chromosomes in the GnomAD database, including 930 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 0.11 (930 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000438575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 4 publications found

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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
ENSG00000227579	ENST00000438575.7	n.389-83992G>A		intron_variant	Intron 3 of 3	3
ENSG00000227579	ENST00000458070.1	n.437-83992G>A		intron_variant	Intron 3 of 3	5
ENSG00000227579	ENST00000654501.1	n.195+78706G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16043 AN: 151996 Hom.: 931 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.106 AC: 16052 AN: 152114 Hom.: 930 Cov.: 32 AF XY: 0.106 AC XY: 7854 AN XY: 74354

African (AFR) AF: 0.0727 AC: 3019 AN: 41508

American (AMR) AF: 0.119 AC: 1825 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3470

East Asian (EAS) AF: 0.0568 AC: 294 AN: 5172

South Asian (SAS) AF: 0.107 AC: 514 AN: 4824

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10564

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8333 AN: 67990

Other (OTH) AF: 0.128 AC: 270 AN: 2108

Alfa AF: 0.119 Hom.: 1260

Bravo AF: 0.105

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs12140698; hg19: chr1-177446916;