2-39780656-T-C

Variant names:

• chr2-39780656-T-C
• rs2192712

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 0.932 in 152,272 control chromosomes in the GnomAD database, including 66,415 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 0.93 (66415 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.932 AC: 141823 AN: 152154 Hom.: 66382 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.932 AC: 141912 AN: 152272 Hom.: 66415 Cov.: 32 AF XY: 0.935 AC XY: 69603 AN XY: 74474

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.981

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.941

Alfa AF: 0.943 Hom.: 16033

Bravo AF: 0.926

Asia WGS AF: 0.957 AC: 3329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
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: rs2192712; hg19: chr2-40007796;