rs1841055

Variant names:

• chr4-68993307-A-C
• rs1841055

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 0.612 in 152,024 control chromosomes in the GnomAD database, including 33,019 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 0.61 (33019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.795 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: 0.612 AC: 93031 AN: 151906 Hom.: 33010 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.612 AC: 93064 AN: 152024 Hom.: 33019 Cov.: 32 AF XY: 0.610 AC XY: 45325 AN XY: 74292

African (AFR) AF: 0.267 AC: 11084 AN: 41436

American (AMR) AF: 0.644 AC: 9827 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2295 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5154

South Asian (SAS) AF: 0.676 AC: 3255 AN: 4818

European-Finnish (FIN) AF: 0.828 AC: 8755 AN: 10580

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54455 AN: 67990

Other (OTH) AF: 0.620 AC: 1311 AN: 2114

Alfa AF: 0.688 Hom.: 9615

Bravo AF: 0.578

Asia WGS AF: 0.476 AC: 1657 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.41
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1841055; hg19: chr4-69859025;