chr6-139457745-A-G

Variant names:

• chr6-139457745-A-G
• rs2286936
• ENST00000654256.2:n.403T>C

Variant summary

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

The ENST00000654256.2(LINC01625):​n.403T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,150 control chromosomes in the GnomAD database, including 3,259 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 0.20 (3259 hom., cov: 32)
• Consequence: LINC01625 ENST00000654256.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 2 publications found

Genes affected

LINC01625 (HGNC:52052): (long intergenic non-protein coding RNA 1625)

ENSG00000226571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986651	XR_001744382.1	n.*43A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01625	ENST00000654256.2	n.403T>C		non_coding_transcript_exon_variant	Exon 4 of 4
LINC01625	ENST00000655740.2	n.498T>C		non_coding_transcript_exon_variant	Exon 4 of 4
LINC01625	ENST00000658080.1	n.490T>C		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30169 AN: 152030 Hom.: 3245 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.199 AC: 30223 AN: 152150 Hom.: 3259 Cov.: 32 AF XY: 0.202 AC XY: 15038 AN XY: 74372

African (AFR) AF: 0.241 AC: 9988 AN: 41508

American (AMR) AF: 0.222 AC: 3390 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.374 AC: 1935 AN: 5174

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4820

European-Finnish (FIN) AF: 0.163 AC: 1729 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10835 AN: 68010

Other (OTH) AF: 0.203 AC: 429 AN: 2116

Alfa AF: 0.178 Hom.: 1370

Bravo AF: 0.204

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.36
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2286936; hg19: chr6-139778882;