chr1-169632043-C-T

Variant names:

• chr1-169632043-C-T
• rs1800805

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 0.309 in 151,988 control chromosomes in the GnomAD database, including 8,165 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 0.31 (8165 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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 (NFE) allele frequency at 95% confidence interval = 0.401 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: 0.309 AC: 46924 AN: 151870 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.309 AC: 46923 AN: 151988 Hom.: 8165 Cov.: 32 AF XY: 0.303 AC XY: 22481 AN XY: 74294

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.336

Alfa AF: 0.387 Hom.: 19789

Bravo AF: 0.299

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800805; hg19: chr1-169601281;