rs2334946

Variant names:

• chr13-22653921-T-C
• rs2334946
• ENST00000815334.1:n.440-2161A>G

Variant summary

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

The ENST00000815334.1(ENSG00000306102):​n.440-2161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,040 control chromosomes in the GnomAD database, including 12,649 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 0.38 (12649 hom., cov: 32)
• Consequence: ENSG00000306102 ENST00000815334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 5 publications found

Genes affected

ENSG00000306102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815334.1. 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
	ENSG00000306102	ENST00000815334.1		n.440-2161A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58101 AN: 151922 Hom.: 12623 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.383 AC: 58174 AN: 152040 Hom.: 12649 Cov.: 32 AF XY: 0.382 AC XY: 28432 AN XY: 74338

African (AFR) AF: 0.598 AC: 24809 AN: 41456

American (AMR) AF: 0.302 AC: 4620 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3468

East Asian (EAS) AF: 0.335 AC: 1733 AN: 5174

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4816

European-Finnish (FIN) AF: 0.412 AC: 4356 AN: 10564

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19710 AN: 67956

Other (OTH) AF: 0.356 AC: 750 AN: 2108

Alfa AF: 0.305 Hom.: 12643

Bravo AF: 0.383

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.39
PhyloP100		-1.9

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: rs2334946;

hg19: chr13-23228060;