rs4658149

Variant names:

• chr1-89392631-C-A
• rs4658149

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 0.203 in 152,022 control chromosomes in the GnomAD database, including 3,931 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 0.20 (3931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 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: 0.203 AC: 30910 AN: 151904 Hom.: 3927 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.203 AC: 30915 AN: 152022 Hom.: 3931 Cov.: 32 AF XY: 0.201 AC XY: 14956 AN XY: 74288

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0206

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.213

Alfa AF: 0.251 Hom.: 2927

Bravo AF: 0.207

Asia WGS AF: 0.0990 AC: 345 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4658149; hg19: chr1-89858190; COSMIC: COSV68969218;