rs6736587

Variant names:

• chr2-81628601-A-C
• rs6736587
• NR_187691.1:n.497+79854A>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.497+79854A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,814 control chromosomes in the GnomAD database, including 15,074 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 0.41 (15074 hom., cov: 31)
• Consequence: LOC102724542 NR_187691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 10 publications found

Genes affected

LOC102724542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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.497+79854A>C		intron	N/A
	LOC102724542	NR_187692.1		n.575+48992A>C		intron	N/A
	LOC102724542	NR_187693.1		n.497+79854A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61876 AN: 151696 Hom.: 15019 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.408 AC: 61979 AN: 151814 Hom.: 15074 Cov.: 31 AF XY: 0.397 AC XY: 29482 AN XY: 74188

African (AFR) AF: 0.688 AC: 28472 AN: 41386

American (AMR) AF: 0.266 AC: 4046 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1296 AN: 3470

East Asian (EAS) AF: 0.178 AC: 914 AN: 5138

South Asian (SAS) AF: 0.129 AC: 623 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3298 AN: 10516

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22060 AN: 67940

Other (OTH) AF: 0.344 AC: 724 AN: 2104

Alfa AF: 0.367 Hom.: 19399

Bravo AF: 0.420

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.71
PhyloP100		-0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6736587; hg19: chr2-81855725;