chr2-24931117-T-C

Variant names:

• chr2-24931117-T-C
• rs6726261
• ENST00000841804.1:n.189+6914T>C

Variant summary

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

The ENST00000841804.1(ENSG00000309511):​n.189+6914T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,076 control chromosomes in the GnomAD database, including 15,252 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 0.42 (15252 hom., cov: 32)
• Consequence: ENSG00000309511 ENST00000841804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 11 publications found

Genes affected

ENSG00000309511 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841804.1. 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
	ENSG00000309511	ENST00000841804.1		n.189+6914T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64414 AN: 151958 Hom.: 15210 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.424 AC: 64507 AN: 152076 Hom.: 15252 Cov.: 32 AF XY: 0.416 AC XY: 30930 AN XY: 74346

African (AFR) AF: 0.640 AC: 26556 AN: 41480

American (AMR) AF: 0.288 AC: 4399 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 967 AN: 3464

East Asian (EAS) AF: 0.309 AC: 1600 AN: 5176

South Asian (SAS) AF: 0.443 AC: 2132 AN: 4818

European-Finnish (FIN) AF: 0.313 AC: 3309 AN: 10564

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24410 AN: 67978

Other (OTH) AF: 0.400 AC: 845 AN: 2110

Alfa AF: 0.376 Hom.: 35201

Bravo AF: 0.428

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.14
PhyloP100		-1.0

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: rs6726261;

hg19: chr2-25153986;