rs2502397

Variant names:

• chr6-113141177-C-T
• rs2502397
• ENST00000722487.1:n.139+14324C>T

Variant summary

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

The ENST00000722487.1(ENSG00000287728):​n.139+14324C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,880 control chromosomes in the GnomAD database, including 14,311 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 0.43 (14311 hom., cov: 31)
• Consequence: ENSG00000287728 ENST00000722487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• Publications: 1 publications found

Genes affected

ENSG00000287728 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722487.1. 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
	ENSG00000287728	ENST00000722487.1		n.139+14324C>T		intron	N/A
	ENSG00000287728	ENST00000722488.1		n.436+3382C>T		intron	N/A
	ENSG00000287728	ENST00000722489.1		n.82+14329C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65248 AN: 151762 Hom.: 14298 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.430 AC: 65302 AN: 151880 Hom.: 14311 Cov.: 31 AF XY: 0.433 AC XY: 32146 AN XY: 74264

African (AFR) AF: 0.491 AC: 20327 AN: 41394

American (AMR) AF: 0.407 AC: 6214 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3466

East Asian (EAS) AF: 0.484 AC: 2499 AN: 5164

South Asian (SAS) AF: 0.329 AC: 1589 AN: 4826

European-Finnish (FIN) AF: 0.488 AC: 5143 AN: 10538

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26774 AN: 67910

Other (OTH) AF: 0.437 AC: 923 AN: 2112

Alfa AF: 0.417 Hom.: 1678

Bravo AF: 0.431

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.52
PhyloP100		-0.99

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: rs2502397;

hg19: chr6-113462379;

COSMIC: COSV69420641;