1-171353382-C-T

Variant names:

• chr1-171353382-C-T
• rs2011345
• ENST00000785012.1:n.307-2051G>A

Variant summary

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

The ENST00000785012.1(ENSG00000302209):​n.307-2051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,142 control chromosomes in the GnomAD database, including 27,280 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 (27280 hom., cov: 32)
• Consequence: ENSG00000302209 ENST00000785012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 8 publications found

Genes affected

ENSG00000302209 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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
ENSG00000302209	ENST00000785012.1	n.307-2051G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87058 AN: 152024 Hom.: 27231 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.573 AC: 87157 AN: 152142 Hom.: 27280 Cov.: 32 AF XY: 0.573 AC XY: 42593 AN XY: 74372

African (AFR) AF: 0.846 AC: 35158 AN: 41540

American (AMR) AF: 0.464 AC: 7095 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2334 AN: 5178

South Asian (SAS) AF: 0.665 AC: 3206 AN: 4822

European-Finnish (FIN) AF: 0.457 AC: 4828 AN: 10572

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31103 AN: 67960

Other (OTH) AF: 0.532 AC: 1124 AN: 2112

Alfa AF: 0.534 Hom.: 4035

Bravo AF: 0.582

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.23
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2011345; hg19: chr1-171322521;