rs2523822

chr6-29860883-A-G

Variant summary

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

The ENST00000647952.1(ENSG00000290870):n.2063-3445T>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 0.259 in 152,026 control chromosomes in the GnomAD database, including 5,338 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 0.26 (5338 hom., cov: 32)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 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.2063-3445T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39358 AN: 151908 Hom.: 5336 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.259 AC: 39365 AN: 152026 Hom.: 5338 Cov.: 32 AF XY: 0.258 AC XY: 19151 AN XY: 74318

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.233

Alfa AF: 0.288 Hom.: 9288

Bravo AF: 0.252

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	7.7
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523822; hg19: chr6-29828660;