2-44253811-G-C

Position:

• chr2-44253811-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649044.1(ENSG00000285542):​n.1135-21693G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,978 control chromosomes in the GnomAD database, including 39,744 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 0.72 (39744 hom., cov: 32)
• Consequence: ENSG00000285542 ENST00000649044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

ENSG00000285542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44253811G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285542	ENST00000649044.1	n.1135-21693G>C		intron_variant				ENSP00000497083.1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109143 AN: 151862 Hom.: 39702 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.719 AC: 109241 AN: 151978 Hom.: 39744 Cov.: 32 AF XY: 0.714 AC XY: 52995 AN XY: 74272

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.727

Alfa AF: 0.656 Hom.: 1875

Bravo AF: 0.710

Asia WGS AF: 0.641 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4953076; hg19: chr2-44480950;