rs6690434

chr1-182589684-T-G

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 0.359 in 152,002 control chromosomes in the GnomAD database, including 9,938 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 0.36 (9938 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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: 0.360 AC: 54607 AN: 151884 Hom.: 9937 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.359 AC: 54626 AN: 152002 Hom.: 9938 Cov.: 31 AF XY: 0.357 AC XY: 26545 AN XY: 74324

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.351

Alfa AF: 0.386 Hom.: 1433

Bravo AF: 0.348

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.20
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6690434; hg19: chr1-182558819;