1-182589684-T-G

Variant names:

• chr1-182589684-T-G
• rs6690434

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 0.359 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.346 AC: 14321 AN: 41444

American (AMR) AF: 0.287 AC: 4391 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1231 AN: 5156

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4824

European-Finnish (FIN) AF: 0.396 AC: 4191 AN: 10576

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26822 AN: 67938

Other (OTH) AF: 0.351 AC: 740 AN: 2106

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
PhyloP100		-0.29
PromoterAI		-0.054	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6690434; hg19: chr1-182558819;