2-41786600-A-T

Variant names:

• chr2-41786600-A-T
• rs7581465

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 0.482 in 152,034 control chromosomes in the GnomAD database, including 18,146 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 0.48 (18146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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: 0.482 AC: 73250 AN: 151916 Hom.: 18105 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.482 AC: 73342 AN: 152034 Hom.: 18146 Cov.: 32 AF XY: 0.479 AC XY: 35629 AN XY: 74312

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.449

Alfa AF: 0.456 Hom.: 2027

Bravo AF: 0.499

Asia WGS AF: 0.439 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581465; hg19: chr2-42013740;