rs7231041

Variant names:

• chr18-25813140-T-C
• rs7231041

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.209 AC: 8677 AN: 41522

American (AMR) AF: 0.194 AC: 2966 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2137 AN: 5168

South Asian (SAS) AF: 0.293 AC: 1413 AN: 4822

European-Finnish (FIN) AF: 0.410 AC: 4333 AN: 10576

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19752 AN: 67994

Other (OTH) AF: 0.244 AC: 516 AN: 2114

Alfa AF: 0.278 Hom.: 12117

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7231041; hg19: chr18-23393104;