18-38530714-C-T

Variant names:

• chr18-38530714-C-T
• rs7242525

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 0.779 in 152,046 control chromosomes in the GnomAD database, including 46,373 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 0.78 (46373 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 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: 0.779 AC: 118413 AN: 151928 Hom.: 46348 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.779 AC: 118486 AN: 152046 Hom.: 46373 Cov.: 31 AF XY: 0.784 AC XY: 58242 AN XY: 74316

African (AFR) AF: 0.707 AC: 29305 AN: 41456

American (AMR) AF: 0.771 AC: 11785 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2521 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4002 AN: 5136

South Asian (SAS) AF: 0.849 AC: 4090 AN: 4816

European-Finnish (FIN) AF: 0.874 AC: 9254 AN: 10584

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55019 AN: 67988

Other (OTH) AF: 0.768 AC: 1623 AN: 2112

Alfa AF: 0.784 Hom.: 7725

Bravo AF: 0.768

Asia WGS AF: 0.809 AC: 2812 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7242525; hg19: chr18-36110678;