rs17708673

Positions:

• chr7-43029785-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43029785C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000232006	ENST00000585996.5	n.555+14762G>A		intron_variant		5
ENSG00000232006	ENST00000609382.3	n.531-1390G>A		intron_variant		5
ENSG00000232006	ENST00000628203.2	n.190-1390G>A		intron_variant		5

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

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0824

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.123

Alfa AF: 0.149 Hom.: 526

Bravo AF: 0.128

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17708673; hg19: chr7-43069384;