chr2-49914979-A-C

Position:

• chr2-49914979-A-C

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 0.392 in 151,942 control chromosomes in the GnomAD database, including 11,910 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 0.39 (11910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 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: 0.392 AC: 59487 AN: 151824 Hom.: 11897 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.392 AC: 59544 AN: 151942 Hom.: 11910 Cov.: 32 AF XY: 0.395 AC XY: 29324 AN XY: 74246

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.397

Alfa AF: 0.370 Hom.: 19822

Bravo AF: 0.398

Asia WGS AF: 0.472 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs971732; hg19: chr2-50142117;