rs1378624

chr2-196180353-G-A

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 0.277 in 151,944 control chromosomes in the GnomAD database, including 6,158 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 0.28 (6158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.277 AC: 42051 AN: 151826 Hom.: 6151 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.277 AC: 42090 AN: 151944 Hom.: 6158 Cov.: 32 AF XY: 0.276 AC XY: 20473 AN XY: 74258

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.278

Alfa AF: 0.253 Hom.: 8349

Bravo AF: 0.289

Asia WGS AF: 0.194 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.065
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378624; hg19: chr2-197045077;