rs4659175

Positions:

• chr1-119413850-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 0.699 in 152,004 control chromosomes in the GnomAD database, including 37,208 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 0.70 (37208 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.119413850T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106145 AN: 151886 Hom.: 37179 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.699 AC: 106227 AN: 152004 Hom.: 37208 Cov.: 32 AF XY: 0.701 AC XY: 52113 AN XY: 74306

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.676

Alfa AF: 0.693 Hom.: 7001

Bravo AF: 0.704

Asia WGS AF: 0.665 AC: 2312 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4659175; hg19: chr1-119956473;