6-140757987-T-G

Position:

• chr6-140757987-T-G

Variant summary

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

The ENST00000684511.1(ENSG00000288714):​n.687T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,972 control chromosomes in the GnomAD database, including 15,784 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 0.43 (15784 hom., cov: 32)
• Consequence: ENST00000684511.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378027	XR_001744387.3	n.1399T>G		non_coding_transcript_exon_variant	5/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000684511.1	n.687T>G		non_coding_transcript_exon_variant	6/9
	ENST00000650553.2	n.293+58145A>C		intron_variant, non_coding_transcript_variant
	ENST00000682976.1	n.419T>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65277 AN: 151854 Hom.: 15744 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.430 AC: 65373 AN: 151972 Hom.: 15784 Cov.: 32 AF XY: 0.425 AC XY: 31591 AN XY: 74262

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.414

Alfa AF: 0.330 Hom.: 3881

Bravo AF: 0.442

Asia WGS AF: 0.426 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.40
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1568482; hg19: chr6-141079124;