rs3218997

chr3-9749660-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 0.0304 in 152,352 control chromosomes in the GnomAD database, including 108 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 0.030 (108 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0304 (4627/152352) while in subpopulation NFE AF= 0.0455 (3096/68026). AF 95% confidence interval is 0.0442. There are 108 homozygotes in gnomad4. There are 2191 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 106 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: 0.0304 AC: 4623 AN: 152234 Hom.: 106 Cov.: 33

Gnomad AFR AF: 0.00799

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0455

Gnomad OTH AF: 0.0396

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

GnomAD4 genome AF: 0.0304 AC: 4627 AN: 152352 Hom.: 108 Cov.: 33 AF XY: 0.0294 AC XY: 2191 AN XY: 74504

Gnomad4 AFR AF: 0.00796

Gnomad4 AMR AF: 0.0337

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.0260

Gnomad4 NFE AF: 0.0455

Gnomad4 OTH AF: 0.0392

Alfa AF: 0.0349 Hom.: 15

Bravo AF: 0.0300

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	8.7
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3218997; hg19: chr3-9791344;