rs25621

Variant names:

• chr6-139537021-C-CTTCT
• rs25621
• ENST00000775590.1:n.98_101dupTTCT

Variant summary

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

The ENST00000775590.1(ENSG00000226571):​n.98_101dupTTCT 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 0.245 in 151,992 control chromosomes in the GnomAD database, including 4,844 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4844 hom., cov: 24)
• Consequence: ENSG00000226571 ENST00000775590.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 2 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226571	ENST00000775590.1	n.98_101dupTTCT		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000226571	ENST00000775591.1	n.55_58dupTTCT		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000226571	ENST00000775596.1	n.113_116dupTTCT		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37124 AN: 151874 Hom.: 4824 Cov.: 24

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.245 AC: 37178 AN: 151992 Hom.: 4844 Cov.: 24 AF XY: 0.248 AC XY: 18428 AN XY: 74300

African (AFR) AF: 0.228 AC: 9434 AN: 41446

American (AMR) AF: 0.348 AC: 5312 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2051 AN: 5146

South Asian (SAS) AF: 0.260 AC: 1255 AN: 4826

European-Finnish (FIN) AF: 0.235 AC: 2485 AN: 10566

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14760 AN: 67970

Other (OTH) AF: 0.259 AC: 546 AN: 2110

Alfa AF: 0.228 Hom.: 429

Bravo AF: 0.252

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs25621; hg19: chr6-139858158;