rs1497411

Variant names:

• chr3-87300747-C-T
• rs1497411

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 136 gene

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: 0.0355 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

African (AFR) AF: 0.00951 AC: 395 AN: 41552

American (AMR) AF: 0.0277 AC: 424 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.00995 AC: 48 AN: 4822

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10596

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3313 AN: 67960

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0468 Hom.: 243

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1497411; hg19: chr3-87349897;