rs7231041

chr18-25813140-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.268 in 152,166 control chromosomes in the GnomAD database, including 5,900 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 0.27 (5900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40823 AN: 152048 Hom.: 5898 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.268 AC: 40840 AN: 152166 Hom.: 5900 Cov.: 32 AF XY: 0.272 AC XY: 20198 AN XY: 74376

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.244

Alfa AF: 0.272 Hom.: 2635

Bravo AF: 0.248

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
Cadd	Benign	15
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7231041; hg19: chr18-23393104;