rs502601

chr11-118694970-G-A

Variant summary

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

The XR_007062909.1(LOC105369519):n.251+1855G>A 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 0.32 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

Genes affected

LOC105369519 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369519	XR_007062909.1	n.251+1855G>A		intron_variant, non_coding_transcript_variant
LOC105369519	XR_007062910.1	n.205+1855G>A		intron_variant, non_coding_transcript_variant
LOC105369519	XR_948068.3	n.342+1855G>A		intron_variant, non_coding_transcript_variant
LOC105369519	XR_948069.3	n.253+1855G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.337

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs502601; hg19: chr11-118565679;