rs2307838

Variant names:

• chr1-55749937-CTGAA-C
• rs2307838
• ENST00000634769.2:n.274+76621_274+76624delTGAA

Your query was ambiguous. Multiple possible variants found:

• chr1-55749937-CTGAA-C
• chr1-55749937-CTGAA-CTGAATGAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000643167.1(LINC01755):​n.278+76621_278+76624delTGAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (17097 hom., cov: 0)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 3 publications found

Genes affected

LINC01755 (HGNC:52543): (long intergenic non-protein coding RNA 1755)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643167.1. 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
	LINC01755	ENST00000634769.2	TSL:5	n.274+76621_274+76624delTGAA		intron	N/A
	LINC01755	ENST00000643167.1		n.278+76621_278+76624delTGAA		intron	N/A
	LINC01755	ENST00000646341.1		n.298+76621_298+76624delTGAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68057 AN: 151372 Hom.: 17087 Cov.: 0

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.449 AC: 68090 AN: 151490 Hom.: 17097 Cov.: 0 AF XY: 0.449 AC XY: 33236 AN XY: 74000

African (AFR) AF: 0.212 AC: 8749 AN: 41358

American (AMR) AF: 0.603 AC: 9178 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1739 AN: 3460

East Asian (EAS) AF: 0.309 AC: 1584 AN: 5126

South Asian (SAS) AF: 0.403 AC: 1935 AN: 4806

European-Finnish (FIN) AF: 0.515 AC: 5410 AN: 10496

Middle Eastern (MID) AF: 0.479 AC: 139 AN: 290

European-Non Finnish (NFE) AF: 0.559 AC: 37844 AN: 67732

Other (OTH) AF: 0.480 AC: 1008 AN: 2102

Alfa AF: 0.492 Hom.: 2350

Bravo AF: 0.449

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2307838; hg19: chr1-56215610;