rs1370041

Variant names:

• chr3-87040015-G-A
• rs1370041
• ENST00000774840.1:n.272-1456G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-87040015-G-A
• chr3-87040015-G-C
• chr3-87040015-G-T

Variant summary

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

The ENST00000774840.1(LINC00506):​n.272-1456G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,984 control chromosomes in the GnomAD database, including 28,561 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 0.61 (28561 hom., cov: 33)
• Consequence: LINC00506 ENST00000774840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 3 publications found

Genes affected

LINC00506 (HGNC:43557): (long intergenic non-protein coding RNA 506)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774840.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00506	ENST00000774840.1		n.272-1456G>A		intron	N/A
	LINC00506	ENST00000774841.1		n.218-1456G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92058 AN: 151866 Hom.: 28544 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.606 AC: 92122 AN: 151984 Hom.: 28561 Cov.: 33 AF XY: 0.611 AC XY: 45387 AN XY: 74288

African (AFR) AF: 0.461 AC: 19123 AN: 41442

American (AMR) AF: 0.634 AC: 9680 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2363 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3608 AN: 5182

South Asian (SAS) AF: 0.682 AC: 3290 AN: 4822

European-Finnish (FIN) AF: 0.658 AC: 6929 AN: 10538

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 45104 AN: 67936

Other (OTH) AF: 0.601 AC: 1269 AN: 2112

Alfa AF: 0.628 Hom.: 5246

Bravo AF: 0.598

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.88
DANN	Benign	0.44
PhyloP100		-0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1370041;

hg19: chr3-87089165;