rs9914203

Positions:

• chr17-3996349-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0343 in 151,918 control chromosomes in the GnomAD database, including 116 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 0.034 (116 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0343 (5208/151918) while in subpopulation NFE AF= 0.0503 (3420/67944). AF 95% confidence interval is 0.0489. There are 116 homozygotes in gnomad4. There are 2460 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 116 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.3996349G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0343 AC: 5207 AN: 151800 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.00905

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0343 AC: 5208 AN: 151918 Hom.: 116 Cov.: 32 AF XY: 0.0331 AC XY: 2460 AN XY: 74220

Gnomad4 AFR AF: 0.00902

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0450

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.0373

Gnomad4 NFE AF: 0.0503

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0409 Hom.: 21

Bravo AF: 0.0325

Asia WGS AF: 0.00924 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9914203; hg19: chr17-3899643; COSMIC: COSV60070699;