chr6-3957037-A-C

Variant names:

• chr6-3957037-A-C
• rs6597017
• ENST00000845058.1:n.387+14221T>G

Variant summary

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

The ENST00000845058.1(ENSG00000230648):​n.387+14221T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,134 control chromosomes in the GnomAD database, including 35,572 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 0.68 (35572 hom., cov: 33)
• Consequence: ENSG00000230648 ENST00000845058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 4 publications found

Genes affected

ENSG00000230648 (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 (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845058.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230648	ENST00000845058.1		n.387+14221T>G		intron	N/A
	ENSG00000230648	ENST00000845059.1		n.357+14221T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103294 AN: 152016 Hom.: 35545 Cov.: 33

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.679 AC: 103374 AN: 152134 Hom.: 35572 Cov.: 33 AF XY: 0.673 AC XY: 50048 AN XY: 74384

African (AFR) AF: 0.680 AC: 28217 AN: 41498

American (AMR) AF: 0.641 AC: 9789 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2617 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5162

South Asian (SAS) AF: 0.599 AC: 2889 AN: 4822

European-Finnish (FIN) AF: 0.652 AC: 6906 AN: 10584

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48583 AN: 68002

Other (OTH) AF: 0.689 AC: 1453 AN: 2110

Alfa AF: 0.698 Hom.: 45472

Bravo AF: 0.678

Asia WGS AF: 0.498 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.82
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6597017; hg19: chr6-3957271;