chr18-60921894-T-C

Variant names:

• chr18-60921894-T-C
• rs1497965

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 0.562 in 151,800 control chromosomes in the GnomAD database, including 24,649 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 0.56 (24649 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.562 AC: 85174 AN: 151680 Hom.: 24601 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.562 AC: 85270 AN: 151800 Hom.: 24649 Cov.: 31 AF XY: 0.561 AC XY: 41596 AN XY: 74204

African (AFR) AF: 0.688 AC: 28459 AN: 41358

American (AMR) AF: 0.515 AC: 7849 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2354 AN: 5166

South Asian (SAS) AF: 0.390 AC: 1876 AN: 4814

European-Finnish (FIN) AF: 0.597 AC: 6283 AN: 10518

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.518 AC: 35207 AN: 67916

Other (OTH) AF: 0.498 AC: 1049 AN: 2106

Alfa AF: 0.529 Hom.: 47328

Bravo AF: 0.567

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.78
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1497965; hg19: chr18-58589127;