rs1497411

Positions:

• chr3-87300747-C-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 0.0355 in 152,184 control chromosomes in the GnomAD database, including 136 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 0.035 (136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0355 (5402/152184) while in subpopulation NFE AF= 0.0487 (3313/67960). AF 95% confidence interval is 0.0474. There are 136 homozygotes in gnomad4. There are 2625 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 136 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: 0.0355 AC: 5401 AN: 152066 Hom.: 136 Cov.: 32

Gnomad AFR AF: 0.00951

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00974

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0355 AC: 5402 AN: 152184 Hom.: 136 Cov.: 32 AF XY: 0.0353 AC XY: 2625 AN XY: 74404

Gnomad4 AFR AF: 0.00951

Gnomad4 AMR AF: 0.0277

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00995

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0466 Hom.: 182

Bravo AF: 0.0321

Asia WGS AF: 0.00492 AC: 17 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1497411; hg19: chr3-87349897;