6-76702349-G-T

Variant names:

• chr6-76702349-G-T
• rs1457955
• ENST00000790727.1:n.446-13896C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000790727.1(ENSG00000302959):​n.446-13896C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,626 control chromosomes in the GnomAD database, including 3,422 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 0.19 (3422 hom., cov: 31)
• Consequence: ENSG00000302959 ENST00000790727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 5 publications found

Genes affected

ENSG00000302959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790727.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302959	ENST00000790727.1		n.446-13896C>A		intron	N/A
	ENSG00000302959	ENST00000790728.1		n.123-2213C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28396 AN: 151508 Hom.: 3412 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.188 AC: 28430 AN: 151626 Hom.: 3422 Cov.: 31 AF XY: 0.186 AC XY: 13753 AN XY: 74082

African (AFR) AF: 0.334 AC: 13794 AN: 41274

American (AMR) AF: 0.201 AC: 3055 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.0726 AC: 372 AN: 5126

South Asian (SAS) AF: 0.136 AC: 653 AN: 4812

European-Finnish (FIN) AF: 0.105 AC: 1100 AN: 10492

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8716 AN: 67940

Other (OTH) AF: 0.183 AC: 385 AN: 2102

Alfa AF: 0.142 Hom.: 3271

Bravo AF: 0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.40
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1457955; hg19: chr6-77412066;