18-65231430-A-G

Variant names:

• chr18-65231430-A-G
• rs637644

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 0.454 in 151,960 control chromosomes in the GnomAD database, including 16,363 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 0.45 (16363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.454 AC: 68966 AN: 151842 Hom.: 16359 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.454 AC: 69003 AN: 151960 Hom.: 16363 Cov.: 32 AF XY: 0.456 AC XY: 33897 AN XY: 74258

African (AFR) AF: 0.415 AC: 17214 AN: 41438

American (AMR) AF: 0.505 AC: 7709 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4592 AN: 5166

South Asian (SAS) AF: 0.498 AC: 2392 AN: 4808

European-Finnish (FIN) AF: 0.429 AC: 4522 AN: 10546

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29417 AN: 67962

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.442 Hom.: 25308

Bravo AF: 0.463

Asia WGS AF: 0.612 AC: 2128 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.41
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs637644; hg19: chr18-62898666;