rs2734973

chr6-29866171-C-T

Variant summary

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

The ENST00000647952.1(ENSG00000290870):n.2063-8733G>A 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 0.109 in 152,174 control chromosomes in the GnomAD database, including 997 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 0.11 (997 hom., cov: 32)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 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.2063-8733G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16537 AN: 152056 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.109 AC: 16578 AN: 152174 Hom.: 997 Cov.: 32 AF XY: 0.109 AC XY: 8075 AN XY: 74388

Gnomad4 AFR AF: 0.0796

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0553

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.130

Alfa AF: 0.122 Hom.: 881

Bravo AF: 0.111

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734973; hg19: chr6-29833948;