18-71730262-G-C

Variant names:

• chr18-71730262-G-C
• rs10514022

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 0.294 in 151,992 control chromosomes in the GnomAD database, including 7,423 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 0.29 (7423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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: 0.295 AC: 44754 AN: 151872 Hom.: 7436 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.294 AC: 44731 AN: 151992 Hom.: 7423 Cov.: 32 AF XY: 0.292 AC XY: 21692 AN XY: 74274

African (AFR) AF: 0.155 AC: 6409 AN: 41480

American (AMR) AF: 0.368 AC: 5615 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2609 AN: 5152

South Asian (SAS) AF: 0.333 AC: 1604 AN: 4814

European-Finnish (FIN) AF: 0.211 AC: 2230 AN: 10568

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23638 AN: 67950

Other (OTH) AF: 0.302 AC: 637 AN: 2108

Alfa AF: 0.307 Hom.: 968

Bravo AF: 0.300

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.66
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10514022; hg19: chr18-69397498;