2-77924883-C-G

Variant names:

• chr2-77924883-C-G
• rs2116977
• ENST00000667782.1:n.138+14948G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667782.1(ENSG00000227088):​n.138+14948G>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: ENSG00000227088 ENST00000667782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 1 publications found

Genes affected

ENSG00000227088 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.345-49821G>C		intron_variant	Intron 1 of 3
LOC105374817	XR_001739552.2	n.792-33G>C		intron_variant	Intron 5 of 5
LOC105374817	XR_940265.3	n.1052-33G>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227088	ENST00000667782.1	n.138+14948G>C		intron_variant	Intron 2 of 6
ENSG00000227088	ENST00000759916.1	n.270-49821G>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.920 AC: 38214 AN: 41524

American (AMR) AF: 0.836 AC: 12779 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2838 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4593 AN: 5162

South Asian (SAS) AF: 0.897 AC: 4334 AN: 4832

European-Finnish (FIN) AF: 0.857 AC: 9084 AN: 10600

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54766 AN: 67986

Other (OTH) AF: 0.853 AC: 1799 AN: 2108

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2116977; hg19: chr2-78152009;