2-77924883-C-G

Position:

• chr2-77924883-C-G

Variant summary

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

The NR_110288.1(LOC101927967):​n.345-49821G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,170 control chromosomes in the GnomAD database, including 55,189 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 0.85 (55189 hom., cov: 32)
• Consequence: LOC101927967 NR_110288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

ENSG00000227088 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.345-49821G>C		intron_variant
LOC105374817	XR_001739552.2	n.792-33G>C		intron_variant
LOC105374817	XR_940265.3	n.1052-33G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000227088	ENST00000667782.1	n.138+14948G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129257 AN: 152052 Hom.: 55135 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.850 AC: 129370 AN: 152170 Hom.: 55189 Cov.: 32 AF XY: 0.854 AC XY: 63522 AN XY: 74384

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.853

Alfa AF: 0.763 Hom.: 2231

Bravo AF: 0.851

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2116977; hg19: chr2-78152009;