6-10295510-A-G

Variant names:

• chr6-10295510-A-G
• rs7753334
• ENST00000829457.1:n.128-12409T>C

Variant summary

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

The ENST00000829457.1(ENSG00000307859):​n.128-12409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 150,910 control chromosomes in the GnomAD database, including 32,081 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 0.65 (32081 hom., cov: 29)
• Consequence: ENSG00000307859 ENST00000829457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 4 publications found

Genes affected

ENSG00000307859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829457.1. 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
	ENSG00000307859	ENST00000829457.1		n.128-12409T>C		intron	N/A
	ENSG00000307859	ENST00000829458.1		n.45-12409T>C		intron	N/A
	ENSG00000307859	ENST00000829459.1		n.359-12409T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.646 AC: 97353 AN: 150790 Hom.: 32052 Cov.: 29

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.646 AC: 97440 AN: 150910 Hom.: 32081 Cov.: 29 AF XY: 0.648 AC XY: 47791 AN XY: 73698

African (AFR) AF: 0.792 AC: 32562 AN: 41100

American (AMR) AF: 0.556 AC: 8455 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1873 AN: 3454

East Asian (EAS) AF: 0.732 AC: 3711 AN: 5070

South Asian (SAS) AF: 0.577 AC: 2754 AN: 4776

European-Finnish (FIN) AF: 0.669 AC: 6987 AN: 10446

Middle Eastern (MID) AF: 0.538 AC: 155 AN: 288

European-Non Finnish (NFE) AF: 0.584 AC: 39433 AN: 67574

Other (OTH) AF: 0.591 AC: 1239 AN: 2096

Alfa AF: 0.598 Hom.: 92019

Bravo AF: 0.642

Asia WGS AF: 0.625 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0070
DANN	Benign	0.28
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7753334; hg19: chr6-10295743;