rs25621

Positions:

• chr6-139537021-C-CTTCT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.139537021_139537022insTTCT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000226571	ENST00000647815.1	n.134+50406_134+50407insTTCT		intron_variant
ENSG00000226571	ENST00000648888.1	n.98+2605_98+2606insTTCT		intron_variant

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

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.259

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs25621; hg19: chr6-139858158;