rs1662840

Variant names:

• chr4-81235255-C-T
• rs1662840

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 0.374 in 152,034 control chromosomes in the GnomAD database, including 13,820 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 0.37 (13820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 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: 0.374 AC: 56805 AN: 151916 Hom.: 13794 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.374 AC: 56891 AN: 152034 Hom.: 13820 Cov.: 32 AF XY: 0.366 AC XY: 27198 AN XY: 74336

African (AFR) AF: 0.697 AC: 28921 AN: 41466

American (AMR) AF: 0.291 AC: 4442 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3472

East Asian (EAS) AF: 0.186 AC: 961 AN: 5170

South Asian (SAS) AF: 0.205 AC: 987 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2376 AN: 10574

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17365 AN: 67934

Other (OTH) AF: 0.324 AC: 683 AN: 2110

Alfa AF: 0.467 Hom.: 5791

Bravo AF: 0.393

Asia WGS AF: 0.218 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1662840; hg19: chr4-82156409;