rs1845344

Positions:

• chr4-120041230-G-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 0.299 in 152,028 control chromosomes in the GnomAD database, including 6,992 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 0.30 (6992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45380 AN: 151910 Hom.: 6993 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.299 AC: 45387 AN: 152028 Hom.: 6992 Cov.: 32 AF XY: 0.294 AC XY: 21824 AN XY: 74316

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.326

Alfa AF: 0.330 Hom.: 19161

Bravo AF: 0.300

Asia WGS AF: 0.178 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1845344; hg19: chr4-120962385;