rs6736587

chr2-81628601-A-C

Variant summary

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

The XR_007088668.1(LOC102724542):n.667+48992A>C variant causes a intron, non coding transcript 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 XR_007088668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724542	XR_007088668.1	n.667+48992A>C		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940294.2	n.575+48992A>C		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940295.2	n.497+79854A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.344

Alfa AF: 0.365 Hom.: 2067

Bravo AF: 0.420

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.47
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6736587; hg19: chr2-81855725;