rs1519592

Positions:

• chr6-140222499-T-C

Variant summary

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

The ENST00000683950.1(ENSG00000288714):​n.201+73809T>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 0.17 in 152,034 control chromosomes in the GnomAD database, including 2,675 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 0.17 (2675 hom., cov: 32)
• Consequence: ENST00000683950.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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
	ENST00000683950.1	n.201+73809T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25782 AN: 151916 Hom.: 2676 Cov.: 32

Gnomad AFR AF: 0.0651

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.170 AC: 25790 AN: 152034 Hom.: 2675 Cov.: 32 AF XY: 0.170 AC XY: 12653 AN XY: 74310

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.171

Alfa AF: 0.177 Hom.: 319

Bravo AF: 0.166

Asia WGS AF: 0.267 AC: 925 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519592; hg19: chr6-140543636;