rs1378624

Variant names:

• chr2-196180353-G-A
• rs1378624

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;