6-83987392-G-T

Position:

• chr6-83987392-G-T

Variant summary

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

The ENST00000420766.1(ENSG00000228679):​n.30-700G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,076 control chromosomes in the GnomAD database, including 6,496 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 (6496 hom., cov: 32)
• Consequence: ENSG00000228679 ENST00000420766.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

ENSG00000228679 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228679	ENST00000420766.1	n.30-700G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27939 AN: 151958 Hom.: 6473 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.184 AC: 28011 AN: 152076 Hom.: 6496 Cov.: 32 AF XY: 0.180 AC XY: 13394 AN XY: 74366

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.0780

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0618

Gnomad4 NFE AF: 0.0408

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0309 Hom.: 33

Bravo AF: 0.200

Asia WGS AF: 0.0400 AC: 140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7770749; hg19: chr6-84697111;