rs11713590

chr3-5689455-G-A

Variant summary

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

The XR_940571.3(LOC105376939):n.204+1274G>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 0.636 in 152,052 control chromosomes in the GnomAD database, including 31,869 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 0.64 (31869 hom., cov: 32)
• Consequence: LOC105376939 XR_940571.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

Genes affected

LOC105376939 (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 (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376939	XR_940571.3	n.204+1274G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96521 AN: 151936 Hom.: 31807 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.636 AC: 96651 AN: 152052 Hom.: 31869 Cov.: 32 AF XY: 0.639 AC XY: 47473 AN XY: 74330

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.598

Alfa AF: 0.551 Hom.: 38963

Bravo AF: 0.648

Asia WGS AF: 0.756 AC: 2625 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.29
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11713590; hg19: chr3-5731142;