rs2508049

chr6-29856106-A-G

Variant summary

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

The ENST00000647952.1(ENSG00000290870):n.2155+1240T>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 0.107 in 150,404 control chromosomes in the GnomAD database, including 1,141 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 (1141 hom., cov: 33)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375010	XR_926681.2	n.41+1240T>C		intron_variant, non_coding_transcript_variant
LOC105375010	XR_926680.3	n.41+1240T>C		intron_variant, non_coding_transcript_variant
LOC105375010	XR_926682.3	n.41+1240T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647952.1	n.2155+1240T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16130 AN: 150294 Hom.: 1140 Cov.: 33

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.107 AC: 16132 AN: 150404 Hom.: 1141 Cov.: 33 AF XY: 0.103 AC XY: 7539 AN XY: 73510

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.0756

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.104

Alfa AF: 0.152 Hom.: 1068

Bravo AF: 0.101

Asia WGS AF: 0.0670 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.6
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2508049; hg19: chr6-29823883;