rs502601

Variant names:

• chr11-118694970-G-A
• rs502601
• XR_007062909.1:n.251+1855G>A

Variant summary

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

The XR_007062909.1(LOC105369519):​n.251+1855G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,164 control chromosomes in the GnomAD database, including 8,181 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 0.32 (8181 hom., cov: 32)
• Consequence: LOC105369519 XR_007062909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 6 publications found

Genes affected

LOC105369519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48682 AN: 152046 Hom.: 8167 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.320 AC: 48718 AN: 152164 Hom.: 8181 Cov.: 32 AF XY: 0.320 AC XY: 23813 AN XY: 74380

African (AFR) AF: 0.255 AC: 10598 AN: 41516

American (AMR) AF: 0.462 AC: 7065 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1258 AN: 3472

East Asian (EAS) AF: 0.405 AC: 2090 AN: 5166

South Asian (SAS) AF: 0.188 AC: 909 AN: 4824

European-Finnish (FIN) AF: 0.312 AC: 3304 AN: 10596

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22235 AN: 67978

Other (OTH) AF: 0.337 AC: 712 AN: 2112

Alfa AF: 0.329 Hom.: 1043

Bravo AF: 0.336

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.87
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs502601; hg19: chr11-118565679;