rs1484095

Variant names:

• chr18-38137614-A-G
• rs1484095

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 0.581 in 152,104 control chromosomes in the GnomAD database, including 26,816 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 0.58 (26816 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.581 AC: 88352 AN: 151988 Hom.: 26780 Cov.: 33

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.581 AC: 88432 AN: 152104 Hom.: 26816 Cov.: 33 AF XY: 0.583 AC XY: 43369 AN XY: 74374

African (AFR) AF: 0.739 AC: 30670 AN: 41490

American (AMR) AF: 0.664 AC: 10146 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3469 AN: 5160

South Asian (SAS) AF: 0.597 AC: 2880 AN: 4822

European-Finnish (FIN) AF: 0.497 AC: 5266 AN: 10588

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32497 AN: 67980

Other (OTH) AF: 0.569 AC: 1199 AN: 2106

Alfa AF: 0.519 Hom.: 82707

Bravo AF: 0.599

Asia WGS AF: 0.649 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1484095; hg19: chr18-35717578;