2-136176879-A-C

Variant names:

• chr2-136176879-A-C
• rs1519523
• ENST00000805101.1:n.685+49429A>C

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.685+49429A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,056 control chromosomes in the GnomAD database, including 33,159 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 0.65 (33159 hom., cov: 31)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 4 publications found

Genes affected

ENSG00000304642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805101.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304642	ENST00000805101.1		n.685+49429A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98684 AN: 151938 Hom.: 33102 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.650 AC: 98800 AN: 152056 Hom.: 33159 Cov.: 31 AF XY: 0.653 AC XY: 48567 AN XY: 74328

African (AFR) AF: 0.739 AC: 30656 AN: 41492

American (AMR) AF: 0.772 AC: 11795 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2987 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4106 AN: 5182

South Asian (SAS) AF: 0.792 AC: 3826 AN: 4828

European-Finnish (FIN) AF: 0.468 AC: 4942 AN: 10554

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38170 AN: 67940

Other (OTH) AF: 0.715 AC: 1508 AN: 2110

Alfa AF: 0.620 Hom.: 75738

Bravo AF: 0.671

Asia WGS AF: 0.808 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	8.5
DANN	Benign	0.66
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1519523;

hg19: chr2-136934449;