2-75318898-A-T

Position:

• chr2-75318898-A-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 0.146 in 152,164 control chromosomes in the GnomAD database, including 1,848 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 0.15 (1848 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.75318898A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22145 AN: 152046 Hom.: 1845 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.146 AC: 22152 AN: 152164 Hom.: 1848 Cov.: 32 AF XY: 0.145 AC XY: 10820 AN XY: 74400

Gnomad4 AFR AF: 0.0635

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.157

Alfa AF: 0.0786 Hom.: 110

Bravo AF: 0.139

Asia WGS AF: 0.213 AC: 738 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17011067; hg19: chr2-75546024;