rs2149434

Variant names:

• chr13-46904209-A-C
• rs2149434
• ENST00000778995.1:n.111+11666A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-46904209-A-C
• chr13-46904209-A-T

Variant summary

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

The ENST00000778995.1(ENSG00000301465):​n.111+11666A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,010 control chromosomes in the GnomAD database, including 24,085 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 0.56 (24085 hom., cov: 32)
• Consequence: ENSG00000301465 ENST00000778995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 4 publications found

Genes affected

ENSG00000301465 (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 (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778995.1. 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
	ENSG00000301465	ENST00000778995.1		n.111+11666A>C		intron	N/A
	ENSG00000301465	ENST00000778996.1		n.122+11605A>C		intron	N/A
	ENSG00000301465	ENST00000778997.1		n.120+8465A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85363 AN: 151892 Hom.: 24071 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.562 AC: 85408 AN: 152010 Hom.: 24085 Cov.: 32 AF XY: 0.561 AC XY: 41717 AN XY: 74306

African (AFR) AF: 0.503 AC: 20868 AN: 41460

American (AMR) AF: 0.613 AC: 9372 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2101 AN: 3468

East Asian (EAS) AF: 0.621 AC: 3206 AN: 5162

South Asian (SAS) AF: 0.498 AC: 2400 AN: 4816

European-Finnish (FIN) AF: 0.576 AC: 6073 AN: 10538

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39494 AN: 67968

Other (OTH) AF: 0.561 AC: 1187 AN: 2114

Alfa AF: 0.576 Hom.: 27904

Bravo AF: 0.561

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
DANN	Benign	0.64
PhyloP100		1.5

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: rs2149434;

hg19: chr13-47478344;