rs3115619

Positions:

• chr6-29875102-A-G
• chr6-29875102-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647952.1(ENSG00000290870):​n.2062+8452T>C 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 0.62 in 150,596 control chromosomes in the GnomAD database, including 29,027 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 0.62 (29027 hom., cov: 27)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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
	ENST00000647952.1	n.2062+8452T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.620 AC: 93290 AN: 150482 Hom.: 28992 Cov.: 27

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.620 AC: 93372 AN: 150596 Hom.: 29027 Cov.: 27 AF XY: 0.613 AC XY: 45053 AN XY: 73534

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.615

Alfa AF: 0.638 Hom.: 6470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3115619; hg19: chr6-29842879;