rs2739733

chr8-18145371-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0292 in 152,212 control chromosomes in the GnomAD database, including 100 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 0.029 (100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0292 (4439/152212) while in subpopulation SAS AF= 0.045 (217/4820). AF 95% confidence interval is 0.0401. There are 100 homozygotes in gnomad4. There are 2207 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 100 gene

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: 0.0292 AC: 4447 AN: 152094 Hom.: 100 Cov.: 32

Gnomad AFR AF: 0.00715

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0292 AC: 4439 AN: 152212 Hom.: 100 Cov.: 32 AF XY: 0.0297 AC XY: 2207 AN XY: 74414

Gnomad4 AFR AF: 0.00712

Gnomad4 AMR AF: 0.0235

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0450

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0155 Hom.: 4

Bravo AF: 0.0265

Asia WGS AF: 0.0120 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.34
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2739733; hg19: chr8-18002880;