chr1-203187994-G-A

Variant names:

• chr1-203187994-G-A
• rs6691378

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.188 in 151,790 control chromosomes in the GnomAD database, including 3,237 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 0.19 (3237 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 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: 0.188 AC: 28520 AN: 151672 Hom.: 3224 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.188 AC: 28548 AN: 151790 Hom.: 3237 Cov.: 31 AF XY: 0.188 AC XY: 13963 AN XY: 74150

African (AFR) AF: 0.277 AC: 11462 AN: 41342

American (AMR) AF: 0.299 AC: 4569 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 525 AN: 3464

East Asian (EAS) AF: 0.296 AC: 1524 AN: 5148

South Asian (SAS) AF: 0.147 AC: 703 AN: 4790

European-Finnish (FIN) AF: 0.0688 AC: 727 AN: 10566

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8420 AN: 67922

Other (OTH) AF: 0.194 AC: 407 AN: 2098

Alfa AF: 0.158 Hom.: 3348

Bravo AF: 0.213

Asia WGS AF: 0.220 AC: 762 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	0.76
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6691378; hg19: chr1-203157122;