rs7234864

Variant names:

• chr18-60067625-C-T
• rs7234864

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.313 in 152,024 control chromosomes in the GnomAD database, including 8,413 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 0.31 (8413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 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: 0.313 AC: 47496 AN: 151906 Hom.: 8401 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.313 AC: 47560 AN: 152024 Hom.: 8413 Cov.: 32 AF XY: 0.308 AC XY: 22857 AN XY: 74318

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.302

Alfa AF: 0.266 Hom.: 9476

Bravo AF: 0.321

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7234864; hg19: chr18-57734857;