rs4659175

Variant names:

• chr1-119413850-T-C
• rs4659175

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;