rs3763338

Variant names:

• chr6-28926534-G-A
• rs3763338
• ENST00000824165.1:n.267+3562G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-28926534-G-A
• chr6-28926534-G-C
• chr6-28926534-G-T

Variant summary

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

The ENST00000824165.1(LINC01556):​n.267+3562G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,226 control chromosomes in the GnomAD database, including 1,013 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 0.11 (1013 hom., cov: 32)
• Consequence: LINC01556 ENST00000824165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 15 publications found

Genes affected

LINC01556 (HGNC:21195): (long intergenic non-protein coding RNA 1556)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824165.1. 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
	LINC01556	ENST00000824165.1		n.267+3562G>A		intron	N/A
	LINC01556	ENST00000824166.1		n.227+3562G>A		intron	N/A
	LINC01556	ENST00000824167.1		n.146+2269G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16547 AN: 152108 Hom.: 1011 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.109 AC: 16576 AN: 152226 Hom.: 1013 Cov.: 32 AF XY: 0.109 AC XY: 8145 AN XY: 74418

African (AFR) AF: 0.144 AC: 5962 AN: 41536

American (AMR) AF: 0.114 AC: 1748 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.109 AC: 564 AN: 5180

South Asian (SAS) AF: 0.0810 AC: 391 AN: 4826

European-Finnish (FIN) AF: 0.108 AC: 1139 AN: 10588

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6092 AN: 68014

Other (OTH) AF: 0.109 AC: 229 AN: 2110

Alfa AF: 0.0997 Hom.: 2024

Bravo AF: 0.115

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.78
PhyloP100		-0.39

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: rs3763338;

hg19: chr6-28894311;