rs800065

Variant names:

• chr3-144669333-T-C
• rs800065

Your query was ambiguous. Multiple possible variants found:

• chr3-144669333-T-C
• chr3-144669333-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.35 in 151,830 control chromosomes in the GnomAD database, including 9,534 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 0.35 (9534 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

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: 0.350 AC: 53068 AN: 151710 Hom.: 9522 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.350 AC: 53099 AN: 151830 Hom.: 9534 Cov.: 31 AF XY: 0.345 AC XY: 25626 AN XY: 74190

African (AFR) AF: 0.270 AC: 11201 AN: 41454

American (AMR) AF: 0.346 AC: 5270 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3464

East Asian (EAS) AF: 0.317 AC: 1630 AN: 5136

South Asian (SAS) AF: 0.319 AC: 1534 AN: 4816

European-Finnish (FIN) AF: 0.362 AC: 3820 AN: 10550

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.404 AC: 27439 AN: 67878

Other (OTH) AF: 0.348 AC: 733 AN: 2106

Alfa AF: 0.378 Hom.: 34864

Bravo AF: 0.348

Asia WGS AF: 0.350 AC: 1219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.67
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs800065; hg19: chr3-144388175;