chr1-206763900-G-T

Position:

• chr1-206763900-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 0.196 in 152,156 control chromosomes in the GnomAD database, including 3,440 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 (3440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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: 0.196 AC: 29754 AN: 152036 Hom.: 3439 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.196 AC: 29756 AN: 152156 Hom.: 3440 Cov.: 32 AF XY: 0.190 AC XY: 14167 AN XY: 74386

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.166

Alfa AF: 0.236 Hom.: 940

Bravo AF: 0.186

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6673928; hg19: chr1-206937245;