6-83987392-G-T

Variant names:

• chr6-83987392-G-T
• rs7770749
• ENST00000420766.1:n.30-700G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000228679 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228679	ENST00000420766.1	n.30-700G>T		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.549 AC: 22747 AN: 41450

American (AMR) AF: 0.0780 AC: 1192 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4826

European-Finnish (FIN) AF: 0.0618 AC: 655 AN: 10600

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0408 AC: 2774 AN: 67962

Other (OTH) AF: 0.135 AC: 284 AN: 2110

Alfa AF: 0.0549 Hom.: 149

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
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs7770749; hg19: chr6-84697111;