rs1394344

Positions:

• chr4-45971222-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 0.482 in 151,816 control chromosomes in the GnomAD database, including 18,446 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 0.48 (18446 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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: 0.482 AC: 73079 AN: 151698 Hom.: 18406 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.482 AC: 73193 AN: 151816 Hom.: 18446 Cov.: 31 AF XY: 0.477 AC XY: 35344 AN XY: 74172

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.451

Alfa AF: 0.460 Hom.: 2056

Bravo AF: 0.493

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1394344; hg19: chr4-45973239;