rs17708673

Variant names:

• chr7-43029785-C-T
• rs17708673
• ENST00000585996.5:n.555+14762G>A

Variant summary

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

The ENST00000585996.5(ENSG00000232006):​n.555+14762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,052 control chromosomes in the GnomAD database, including 1,752 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 0.14 (1752 hom., cov: 32)
• Consequence: ENSG00000232006 ENST00000585996.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969
• Publications: 3 publications found

Genes affected

ENSG00000232006 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585996.5. 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
	ENSG00000232006	ENST00000585996.5	TSL:5	n.555+14762G>A		intron	N/A
	ENSG00000232006	ENST00000609382.3	TSL:5	n.531-1390G>A		intron	N/A
	ENSG00000232006	ENST00000628203.2	TSL:5	n.190-1390G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21423 AN: 151934 Hom.: 1750 Cov.: 32

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.141 AC: 21421 AN: 152052 Hom.: 1752 Cov.: 32 AF XY: 0.147 AC XY: 10929 AN XY: 74312

African (AFR) AF: 0.0624 AC: 2589 AN: 41522

American (AMR) AF: 0.148 AC: 2266 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3470

East Asian (EAS) AF: 0.192 AC: 992 AN: 5160

South Asian (SAS) AF: 0.252 AC: 1215 AN: 4814

European-Finnish (FIN) AF: 0.240 AC: 2524 AN: 10538

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11113 AN: 67964

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.147 Hom.: 529

Bravo AF: 0.128

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.84
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs17708673; hg19: chr7-43069384;