6-35562369-A-C

Variant names:

• chr6-35562369-A-C
• rs6917735
• ENST00000722031.1:n.103+17436A>C

Variant summary

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

The ENST00000722031.1(ENSG00000228559):​n.103+17436A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.045 in 152,292 control chromosomes in the GnomAD database, including 230 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 0.045 (230 hom., cov: 32)
• Consequence: ENSG00000228559 ENST00000722031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 3 publications found

Genes affected

ENSG00000228559 (HGNC:58100):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722031.1. 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
	ENSG00000228559	ENST00000722031.1		n.103+17436A>C		intron	N/A
	ENSG00000228559	ENST00000722032.1		n.140+17436A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0449 AC: 6832 AN: 152174 Hom.: 230 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0310

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0249

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0450 AC: 6847 AN: 152292 Hom.: 230 Cov.: 32 AF XY: 0.0435 AC XY: 3239 AN XY: 74460

African (AFR) AF: 0.0978 AC: 4061 AN: 41544

American (AMR) AF: 0.0310 AC: 474 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5186

South Asian (SAS) AF: 0.00622 AC: 30 AN: 4824

European-Finnish (FIN) AF: 0.0152 AC: 162 AN: 10624

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0249 AC: 1694 AN: 68024

Other (OTH) AF: 0.0440 AC: 93 AN: 2112

Alfa AF: 0.0318 Hom.: 149

Bravo AF: 0.0484

Asia WGS AF: 0.0160 AC: 54 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	1.8
DANN	Benign	0.15
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6917735; hg19: chr6-35530146;