6-140223977-G-T

Position:

• chr6-140223977-G-T

Variant summary

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

The ENST00000683950.1(ENSG00000288714):​n.201+75287G>T 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 0.18 in 152,114 control chromosomes in the GnomAD database, including 2,831 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 0.18 (2831 hom., cov: 32)
• Consequence: ENST00000683950.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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+75287G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27299 AN: 151994 Hom.: 2831 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.180 AC: 27313 AN: 152114 Hom.: 2831 Cov.: 32 AF XY: 0.180 AC XY: 13384 AN XY: 74338

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.179

Alfa AF: 0.187 Hom.: 484

Bravo AF: 0.176

Asia WGS AF: 0.284 AC: 982 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1496112; hg19: chr6-140545114;