rs6691378

chr1-203187994-G-A

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 0.188 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

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 (AMR) allele frequency at 95% confidence interval = 0.292 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: 0.188 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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0688

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.194

Alfa AF: 0.171 Hom.: 231

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6691378; hg19: chr1-203157122;