rs4276378

Positions:

• chr5-7244378-A-G
• chr5-7244378-A-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 0.398 in 151,992 control chromosomes in the GnomAD database, including 12,507 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 0.40 (12507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.398 AC: 60422 AN: 151872 Hom.: 12495 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.398 AC: 60461 AN: 151992 Hom.: 12507 Cov.: 32 AF XY: 0.404 AC XY: 30017 AN XY: 74278

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.438

Alfa AF: 0.418 Hom.: 20408

Bravo AF: 0.390

Asia WGS AF: 0.564 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.039
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4276378; hg19: chr5-7244491;