chr1-185461362-G-T

Position:

• chr1-185461362-G-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 0.333 in 151,376 control chromosomes in the GnomAD database, including 9,498 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 0.33 (9498 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50371 AN: 151280 Hom.: 9482 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.333 AC: 50427 AN: 151376 Hom.: 9498 Cov.: 31 AF XY: 0.334 AC XY: 24660 AN XY: 73872

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.308

Alfa AF: 0.260 Hom.: 5274

Bravo AF: 0.347

Asia WGS AF: 0.437 AC: 1519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4323662; hg19: chr1-185430494;