chr2-70583039-C-T

Variant names:

• chr2-70583039-C-T
• rs17005914

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.209 in 152,116 control chromosomes in the GnomAD database, including 4,436 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 0.21 (4436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 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: 0.209 AC: 31825 AN: 151998 Hom.: 4427 Cov.: 32

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.209 AC: 31835 AN: 152116 Hom.: 4436 Cov.: 32 AF XY: 0.219 AC XY: 16303 AN XY: 74330

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.193

Alfa AF: 0.240 Hom.: 657

Bravo AF: 0.192

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17005914; hg19: chr2-70810171;