chr2-73294038-C-T

Position:

• chr2-73294038-C-T

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 0.232 in 151,940 control chromosomes in the GnomAD database, including 7,601 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 0.23 (7601 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35087 AN: 151828 Hom.: 7563 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.232 AC: 35188 AN: 151940 Hom.: 7601 Cov.: 33 AF XY: 0.232 AC XY: 17231 AN XY: 74256

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0563

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.202

Alfa AF: 0.0927 Hom.: 1564

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.79
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6718289; hg19: chr2-73521166;