18-74495461-T-C

Variant names:

• chr18-74495461-T-C
• rs11873377

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 0.109 in 152,152 control chromosomes in the GnomAD database, including 1,558 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 0.11 (1558 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 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: 0.109 AC: 16601 AN: 152034 Hom.: 1557 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.109 AC: 16611 AN: 152152 Hom.: 1558 Cov.: 33 AF XY: 0.107 AC XY: 7989 AN XY: 74394

African (AFR) AF: 0.253 AC: 10505 AN: 41444

American (AMR) AF: 0.0575 AC: 879 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5194

South Asian (SAS) AF: 0.0748 AC: 361 AN: 4824

European-Finnish (FIN) AF: 0.0552 AC: 585 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3739 AN: 68004

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0563 Hom.: 153

Bravo AF: 0.116

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		-1.0
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11873377; hg19: chr18-72162696;