chr1-186671485-C-T

Position:

• chr1-186671485-C-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 0.262 in 152,046 control chromosomes in the GnomAD database, including 7,883 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 0.26 (7883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39810 AN: 151928 Hom.: 7840 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.262 AC: 39911 AN: 152046 Hom.: 7883 Cov.: 32 AF XY: 0.255 AC XY: 18977 AN XY: 74324

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.259

Alfa AF: 0.225 Hom.: 886

Bravo AF: 0.283

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4648308; hg19: chr1-186640617;