rs1378441

Variant names:

• chr5-98408322-C-A
• rs1378441

Your query was ambiguous. Multiple possible variants found:

• chr5-98408322-C-A
• chr5-98408322-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.192 AC: 7959 AN: 41472

American (AMR) AF: 0.376 AC: 5745 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2588 AN: 5142

South Asian (SAS) AF: 0.374 AC: 1796 AN: 4804

European-Finnish (FIN) AF: 0.456 AC: 4807 AN: 10548

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26320 AN: 67968

Other (OTH) AF: 0.363 AC: 766 AN: 2108

Alfa AF: 0.371 Hom.: 33744

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1378441; hg19: chr5-97744026;