rs6691378

Variant names:

• chr1-203187994-G-A
• rs6691378

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 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

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;