rs1378441

Positions:

• chr5-98408322-C-A
• chr5-98408322-C-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 0.341 in 151,988 control chromosomes in the GnomAD database, including 9,606 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 0.34 (9606 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51765 AN: 151870 Hom.: 9602 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.341 AC: 51780 AN: 151988 Hom.: 9606 Cov.: 31 AF XY: 0.345 AC XY: 25650 AN XY: 74296

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.363

Alfa AF: 0.380 Hom.: 14504

Bravo AF: 0.327

Asia WGS AF: 0.398 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
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: rs1378441; hg19: chr5-97744026;