rs7234864

Positions:

• chr18-60067625-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;