rs25630

chr6-14734110-C-CAGchr6-14734110-C-CAGA

Variant summary

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

The ENST00000629853.2(ENSG00000234261):n.313+55879_313+55880insCT variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,018 control chromosomes in the GnomAD database, including 16,355 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (16355 hom., cov: 0)
• Consequence: ENST00000629853.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000629853.2	n.313+55879_313+55880insCT		intron_variant, non_coding_transcript_variant		5
	ENST00000689305.1	n.230+6889_230+6890insCT		intron_variant, non_coding_transcript_variant
	ENST00000702363.1	n.187-2633_187-2632insCT		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56005 AN: 151902 Hom.: 16311 Cov.: 0

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.369 AC: 56103 AN: 152018 Hom.: 16355 Cov.: 0 AF XY: 0.361 AC XY: 26820 AN XY: 74340

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.0856

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.341

Alfa AF: 0.117 Hom.: 257

Bravo AF: 0.404

Asia WGS AF: 0.216 AC: 753 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: rs25630; hg19: chr6-14734341;