chr2-81545870-T-C

Variant names:

• chr2-81545870-T-C
• rs6715049
• ENST00000817540.1:n.373-2748T>C

Variant summary

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

The NR_187691.1(LOC102724542):​n.368-2748T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 150,720 control chromosomes in the GnomAD database, including 11,306 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 0.37 (11306 hom., cov: 29)
• Consequence: LOC102724542 NR_187691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 4 publications found

Genes affected

ENSG00000306384 (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 = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187691.1. 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
	LOC102724542	NR_187691.1		n.368-2748T>C		intron	N/A
	LOC102724542	NR_187692.1		n.368-2748T>C		intron	N/A
	LOC102724542	NR_187693.1		n.368-2748T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306384	ENST00000817540.1		n.373-2748T>C		intron	N/A
	ENSG00000306384	ENST00000817541.1		n.371-2748T>C		intron	N/A
	ENSG00000306384	ENST00000817542.1		n.366-2748T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55072 AN: 150616 Hom.: 11265 Cov.: 29

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.265

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.366 AC: 55156 AN: 150720 Hom.: 11306 Cov.: 29 AF XY: 0.356 AC XY: 26233 AN XY: 73610

African (AFR) AF: 0.554 AC: 22684 AN: 40948

American (AMR) AF: 0.255 AC: 3862 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1004 AN: 3460

East Asian (EAS) AF: 0.175 AC: 899 AN: 5128

South Asian (SAS) AF: 0.112 AC: 536 AN: 4804

European-Finnish (FIN) AF: 0.299 AC: 3068 AN: 10276

Middle Eastern (MID) AF: 0.260 AC: 75 AN: 288

European-Non Finnish (NFE) AF: 0.324 AC: 21935 AN: 67694

Other (OTH) AF: 0.309 AC: 647 AN: 2094

Alfa AF: 0.329 Hom.: 5239

Bravo AF: 0.376

Asia WGS AF: 0.176 AC: 613 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	1.1
DANN	Benign	0.45
PhyloP100		-0.78

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: rs6715049;

hg19: chr2-81772994;