rs1908592

Variant names:

• chr12-41634677-T-C
• rs1908592
• ENST00000779513.1:n.95+8669A>G

Variant summary

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

The ENST00000779513.1(ENSG00000301531):​n.95+8669A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,976 control chromosomes in the GnomAD database, including 1,737 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 0.14 (1737 hom., cov: 32)
• Consequence: ENSG00000301531 ENST00000779513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 2 publications found

Genes affected

ENSG00000301531 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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
ENSG00000301531	ENST00000779513.1	n.95+8669A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21583 AN: 151858 Hom.: 1735 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.142 AC: 21583 AN: 151976 Hom.: 1737 Cov.: 32 AF XY: 0.141 AC XY: 10476 AN XY: 74276

African (AFR) AF: 0.0798 AC: 3307 AN: 41448

American (AMR) AF: 0.140 AC: 2140 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3472

East Asian (EAS) AF: 0.182 AC: 942 AN: 5162

South Asian (SAS) AF: 0.226 AC: 1087 AN: 4804

European-Finnish (FIN) AF: 0.124 AC: 1312 AN: 10570

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11771 AN: 67936

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.151 Hom.: 455

Bravo AF: 0.138

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs1908592; hg19: chr12-42028479;