rs17750424

Variant names:

• chr6-27733343-T-C
• rs17750424
• ENST00000783576.1:n.355+9686A>G

Variant summary

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

The ENST00000783576.1(ENSG00000302043):​n.355+9686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 151,098 control chromosomes in the GnomAD database, including 329 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 0.052 (329 hom., cov: 31)
• Consequence: ENSG00000302043 ENST00000783576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 19 publications found

Genes affected

ENSG00000302043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783576.1. 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
	ENSG00000302043	ENST00000783576.1		n.355+9686A>G		intron	N/A
	ENSG00000302043	ENST00000783577.1		n.203+20716A>G		intron	N/A
	ENSG00000302043	ENST00000783578.1		n.301+9686A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0520 AC: 7854 AN: 150986 Hom.: 329 Cov.: 31

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.0399

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

GnomAD4 genome AF: 0.0520 AC: 7850 AN: 151098 Hom.: 329 Cov.: 31 AF XY: 0.0469 AC XY: 3467 AN XY: 73892

African (AFR) AF: 0.0153 AC: 633 AN: 41388

American (AMR) AF: 0.0346 AC: 526 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.0377 AC: 376 AN: 9980

Middle Eastern (MID) AF: 0.00690 AC: 2 AN: 290

European-Non Finnish (NFE) AF: 0.0890 AC: 6034 AN: 67782

Other (OTH) AF: 0.0395 AC: 83 AN: 2102

Alfa AF: 0.0886 Hom.: 370

Bravo AF: 0.0506

Asia WGS AF: 0.00434 AC: 16 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs17750424; hg19: chr6-27701122;