chr18-65415362-T-G

Variant names:

• chr18-65415362-T-G
• rs565973

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 0.506 in 151,462 control chromosomes in the GnomAD database, including 20,478 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 0.51 (20478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 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: 0.506 AC: 76576 AN: 151342 Hom.: 20452 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.506 AC: 76661 AN: 151462 Hom.: 20478 Cov.: 32 AF XY: 0.500 AC XY: 36999 AN XY: 74018

African (AFR) AF: 0.676 AC: 27984 AN: 41404

American (AMR) AF: 0.478 AC: 7251 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1439 AN: 3458

East Asian (EAS) AF: 0.181 AC: 921 AN: 5080

South Asian (SAS) AF: 0.397 AC: 1908 AN: 4810

European-Finnish (FIN) AF: 0.372 AC: 3941 AN: 10588

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31679 AN: 67642

Other (OTH) AF: 0.494 AC: 1038 AN: 2100

Alfa AF: 0.475 Hom.: 32438

Bravo AF: 0.518

Asia WGS AF: 0.362 AC: 1260 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	2.6
DANN	Benign	0.58
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs565973; hg19: chr18-63082598;