NR_187691.1:n.497+66795T>C

Variant names:

• chr2-81615542-T-C
• rs6547378
• NR_187691.1:n.497+66795T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_187691.1(LOC102724542):​n.497+66795T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,078 control chromosomes in the GnomAD database, including 12,246 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 (12246 hom., cov: 32)
• Consequence: LOC102724542 NR_187691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724542	NR_187691.1	n.497+66795T>C		intron_variant	Intron 2 of 3
LOC102724542	NR_187692.1	n.575+35933T>C		intron_variant	Intron 3 of 4
LOC102724542	NR_187693.1	n.497+66795T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55917 AN: 151960 Hom.: 12199 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.368 AC: 56014 AN: 152078 Hom.: 12246 Cov.: 32 AF XY: 0.358 AC XY: 26613 AN XY: 74356

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0544

Gnomad4 SAS AF: 0.0903

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.298

Alfa AF: 0.319 Hom.: 2710

Bravo AF: 0.376

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6547378; hg19: chr2-81842666;