rs1185678

chr1-190874079-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 0.0697 in 151,920 control chromosomes in the GnomAD database, including 1,064 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 0.070 (1064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.0697 AC: 10579 AN: 151802 Hom.: 1063 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.00877

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0697 AC: 10594 AN: 151920 Hom.: 1064 Cov.: 32 AF XY: 0.0674 AC XY: 5008 AN XY: 74256

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0295

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.0450

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00877

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0471 Hom.: 96

Bravo AF: 0.0798

Asia WGS AF: 0.0360 AC: 126 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1185678; hg19: chr1-190843209;