2-44041661-C-T

Position:

• chr2-44041661-C-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 0.787 in 152,138 control chromosomes in the GnomAD database, including 47,683 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 0.79 (47683 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44041661C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119684 AN: 152018 Hom.: 47639 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.787 AC: 119779 AN: 152138 Hom.: 47683 Cov.: 32 AF XY: 0.784 AC XY: 58334 AN XY: 74394

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.781

Alfa AF: 0.751 Hom.: 85138

Bravo AF: 0.788

Asia WGS AF: 0.611 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.011
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4953045; hg19: chr2-44268800;