rs17797449

Positions:

• chr4-145447634-T-C

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 0.313 in 150,960 control chromosomes in the GnomAD database, including 9,068 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 0.31 (9068 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.935

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.145447634T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286420	ENST00000658284.1	n.255-2198A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47178 AN: 150842 Hom.: 9066 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.313 AC: 47179 AN: 150960 Hom.: 9068 Cov.: 32 AF XY: 0.309 AC XY: 22811 AN XY: 73740

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0985

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.308

Alfa AF: 0.377 Hom.: 1504

Bravo AF: 0.283

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17797449; hg19: chr4-146368786;