rs7240004

Variant names:

• chr18-48868651-A-G
• rs7240004

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 0.433 in 152,034 control chromosomes in the GnomAD database, including 14,631 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 0.43 (14631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 45 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 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: 0.433 AC: 65710 AN: 151916 Hom.: 14602 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.433 AC: 65790 AN: 152034 Hom.: 14631 Cov.: 32 AF XY: 0.435 AC XY: 32321 AN XY: 74326

African (AFR) AF: 0.536 AC: 22212 AN: 41466

American (AMR) AF: 0.412 AC: 6286 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2670 AN: 5160

South Asian (SAS) AF: 0.496 AC: 2386 AN: 4812

European-Finnish (FIN) AF: 0.380 AC: 4023 AN: 10578

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25346 AN: 67960

Other (OTH) AF: 0.437 AC: 921 AN: 2108

Alfa AF: 0.399 Hom.: 38370

Bravo AF: 0.441

Asia WGS AF: 0.558 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.81
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7240004; hg19: chr18-46395022;