rs1845344

Variant names:

• chr4-120041230-G-T
• rs1845344

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 0.299 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
• Publications: 11 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.285 AC: 11800 AN: 41472

American (AMR) AF: 0.263 AC: 4010 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3466

East Asian (EAS) AF: 0.114 AC: 590 AN: 5184

South Asian (SAS) AF: 0.228 AC: 1096 AN: 4814

European-Finnish (FIN) AF: 0.258 AC: 2721 AN: 10554

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22900 AN: 67960

Other (OTH) AF: 0.326 AC: 689 AN: 2116

Alfa AF: 0.325 Hom.: 38021

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1845344; hg19: chr4-120962385;