rs1914986

Positions:

• chr17-56730348-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 0.272 in 152,186 control chromosomes in the GnomAD database, including 11,323 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 0.27 (11323 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56730348C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41379 AN: 152068 Hom.: 11286 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.272 AC: 41465 AN: 152186 Hom.: 11323 Cov.: 33 AF XY: 0.270 AC XY: 20064 AN XY: 74408

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.204

Alfa AF: 0.190 Hom.: 1042

Bravo AF: 0.297

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.064
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1914986; hg19: chr17-54807709;