6-100353935-G-C

Variant names:

• chr6-100353935-G-C
• rs7768342
• ENST00000837451.1:n.435+752C>G

Variant summary

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

The ENST00000837451.1(ENSG00000308943):​n.435+752C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,506 control chromosomes in the GnomAD database, including 16,623 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 0.46 (16623 hom., cov: 31)
• Consequence: ENSG00000308943 ENST00000837451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 2 publications found

Genes affected

ENSG00000308943 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837451.1. 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
	ENSG00000308943	ENST00000837451.1		n.435+752C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70125 AN: 151386 Hom.: 16608 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.463 AC: 70177 AN: 151506 Hom.: 16623 Cov.: 31 AF XY: 0.462 AC XY: 34222 AN XY: 74020

African (AFR) AF: 0.537 AC: 22142 AN: 41226

American (AMR) AF: 0.369 AC: 5631 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1341 AN: 5136

South Asian (SAS) AF: 0.576 AC: 2769 AN: 4804

European-Finnish (FIN) AF: 0.444 AC: 4652 AN: 10466

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30580 AN: 67826

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.291 Hom.: 671

Bravo AF: 0.457

Asia WGS AF: 0.413 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.56
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs7768342; hg19: chr6-100801811;