chr2-207627419-A-T

Position:

• chr2-207627419-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 0.349 in 151,776 control chromosomes in the GnomAD database, including 9,563 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 (9563 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

(HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.207627419A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52949 AN: 151658 Hom.: 9544 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.349 AC: 53004 AN: 151776 Hom.: 9563 Cov.: 31 AF XY: 0.354 AC XY: 26226 AN XY: 74178

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.330

Alfa AF: 0.344 Hom.: 1129

Bravo AF: 0.349

Asia WGS AF: 0.438 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.70
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2551941; hg19: chr2-208492143;