rs1845830

Variant names:

• chr5-18629300-G-A
• rs1845830

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 0.355 in 151,712 control chromosomes in the GnomAD database, including 10,099 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 0.35 (10099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 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: 0.354 AC: 53709 AN: 151596 Hom.: 10074 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.355 AC: 53790 AN: 151712 Hom.: 10099 Cov.: 32 AF XY: 0.362 AC XY: 26814 AN XY: 74158

African (AFR) AF: 0.416 AC: 17185 AN: 41358

American (AMR) AF: 0.479 AC: 7295 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2094 AN: 5152

South Asian (SAS) AF: 0.476 AC: 2294 AN: 4816

European-Finnish (FIN) AF: 0.311 AC: 3273 AN: 10528

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19589 AN: 67838

Other (OTH) AF: 0.363 AC: 765 AN: 2108

Alfa AF: 0.318 Hom.: 10698

Bravo AF: 0.366

Asia WGS AF: 0.452 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.63
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1845830; hg19: chr5-18629409;