rs2850700

Variant names:

• chr18-65450406-C-T
• rs2850700

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 0.444 in 151,744 control chromosomes in the GnomAD database, including 15,102 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 0.44 (15102 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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: 0.444 AC: 67361 AN: 151626 Hom.: 15085 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.444 AC: 67415 AN: 151744 Hom.: 15102 Cov.: 31 AF XY: 0.444 AC XY: 32913 AN XY: 74128

African (AFR) AF: 0.440 AC: 18243 AN: 41418

American (AMR) AF: 0.400 AC: 6078 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1961 AN: 3466

East Asian (EAS) AF: 0.594 AC: 3060 AN: 5150

South Asian (SAS) AF: 0.462 AC: 2224 AN: 4812

European-Finnish (FIN) AF: 0.402 AC: 4236 AN: 10528

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30002 AN: 67842

Other (OTH) AF: 0.447 AC: 944 AN: 2112

Alfa AF: 0.428 Hom.: 3993

Bravo AF: 0.450

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.21
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2850700; hg19: chr18-63117642;