chr2-237858561-A-T

Position:

• chr2-237858561-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 0.431 in 152,042 control chromosomes in the GnomAD database, including 14,679 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 0.43 (14679 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65501 AN: 151924 Hom.: 14645 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.431 AC: 65596 AN: 152042 Hom.: 14679 Cov.: 33 AF XY: 0.435 AC XY: 32317 AN XY: 74310

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.416

Alfa AF: 0.234 Hom.: 502

Bravo AF: 0.444

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.32
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754701; hg19: chr2-238767204;