2-44836421-C-G

Variant names:

• chr2-44836421-C-G
• rs341607

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 0.602 in 152,096 control chromosomes in the GnomAD database, including 28,751 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 0.60 (28751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91496 AN: 151978 Hom.: 28731 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.602 AC: 91565 AN: 152096 Hom.: 28751 Cov.: 32 AF XY: 0.610 AC XY: 45359 AN XY: 74352

African (AFR) AF: 0.721 AC: 29926 AN: 41488

American (AMR) AF: 0.683 AC: 10448 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1573 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4707 AN: 5182

South Asian (SAS) AF: 0.753 AC: 3631 AN: 4822

European-Finnish (FIN) AF: 0.562 AC: 5931 AN: 10554

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33508 AN: 67974

Other (OTH) AF: 0.590 AC: 1244 AN: 2110

Alfa AF: 0.400 Hom.: 976

Bravo AF: 0.617

Asia WGS AF: 0.773 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
DANN	Benign	0.39
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs341607; hg19: chr2-45063560;