1-171090116-T-A

Variant names:

• chr1-171090116-T-A
• rs12404218
• ENST00000653116.1:n.542+77988A>T

Variant summary

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

The ENST00000653116.1(ENSG00000231424):​n.542+77988A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,248 control chromosomes in the GnomAD database, including 1,073 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 0.10 (1073 hom., cov: 32)
• Consequence: ENSG00000231424 ENST00000653116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 4 publications found

Genes affected

ENSG00000231424 (HGNC:40240):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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
ENSG00000231424	ENST00000653116.1	n.542+77988A>T		intron_variant	Intron 3 of 3
ENSG00000231424	ENST00000664920.1	n.681+31634A>T		intron_variant	Intron 4 of 5
ENSG00000231424	ENST00000669750.1	n.533+77988A>T		intron_variant	Intron 3 of 4
ENSG00000231424	ENST00000670085.1	n.371+77988A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15674 AN: 152130 Hom.: 1065 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.103 AC: 15700 AN: 152248 Hom.: 1073 Cov.: 32 AF XY: 0.106 AC XY: 7888 AN XY: 74462

African (AFR) AF: 0.124 AC: 5155 AN: 41534

American (AMR) AF: 0.203 AC: 3104 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5174

South Asian (SAS) AF: 0.194 AC: 935 AN: 4822

European-Finnish (FIN) AF: 0.0497 AC: 528 AN: 10618

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4228 AN: 68016

Other (OTH) AF: 0.102 AC: 215 AN: 2116

Alfa AF: 0.0841 Hom.: 87

Bravo AF: 0.114

Asia WGS AF: 0.218 AC: 756 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs12404218; hg19: chr1-171059257;