rs3218997

Variant names:

• chr3-9749660-C-T
• rs3218997

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 0.0304 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 108 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: 0.0304 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

African (AFR) AF: 0.00796 AC: 331 AN: 41574

American (AMR) AF: 0.0337 AC: 516 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5192

South Asian (SAS) AF: 0.0313 AC: 151 AN: 4832

European-Finnish (FIN) AF: 0.0260 AC: 276 AN: 10630

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0455 AC: 3096 AN: 68026

Other (OTH) AF: 0.0392 AC: 83 AN: 2116

Alfa AF: 0.0305 Hom.: 56

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
PhyloP100		0.079
PromoterAI		0.029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3218997; hg19: chr3-9791344;