rs2734975

chr6-29865476-C-Achr6-29865476-C-G

Variant summary

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

The ENST00000647952.1(ENSG00000290870):n.2063-8038G>T 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 0.482 in 152,042 control chromosomes in the GnomAD database, including 17,742 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 0.48 (17742 hom., cov: 33)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

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 (AMR) allele frequency at 95% confidence interval = 0.506 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.2063-8038G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73192 AN: 151924 Hom.: 17715 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.482 AC: 73256 AN: 152042 Hom.: 17742 Cov.: 33 AF XY: 0.480 AC XY: 35641 AN XY: 74302

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.474

Alfa AF: 0.487 Hom.: 3317

Bravo AF: 0.493

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.6
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734975; hg19: chr6-29833253;