rs3212247

Variant names:

• chr14-24340589-A-G
• rs3212247

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 0.126 in 152,190 control chromosomes in the GnomAD database, including 1,610 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 0.13 (1610 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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: 0.126 AC: 19135 AN: 152072 Hom.: 1602 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.126 AC: 19172 AN: 152190 Hom.: 1610 Cov.: 33 AF XY: 0.131 AC XY: 9785 AN XY: 74414

African (AFR) AF: 0.204 AC: 8446 AN: 41496

American (AMR) AF: 0.0915 AC: 1399 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1575 AN: 5168

South Asian (SAS) AF: 0.196 AC: 947 AN: 4820

European-Finnish (FIN) AF: 0.130 AC: 1382 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0697 AC: 4739 AN: 68014

Other (OTH) AF: 0.115 AC: 242 AN: 2112

Alfa AF: 0.0873 Hom.: 1252

Bravo AF: 0.124

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.58
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs3212247; hg19: chr14-24809795;