2-77798450-G-T

Variant names:

• chr2-77798450-G-T
• rs2171325
• ENST00000667782.1:n.343+41319C>A

Variant summary

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

The NR_110288.1(LOC101927967):​n.549+41319C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 151,656 control chromosomes in the GnomAD database, including 619 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 0.060 (619 hom., cov: 32)
• Consequence: LOC101927967 NR_110288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_110288.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927967	NR_110288.1		n.549+41319C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227088	ENST00000667782.1		n.343+41319C>A		intron	N/A
	ENSG00000227088	ENST00000828171.1		n.50+25882C>A		intron	N/A
	ENSG00000227088	ENST00000828172.1		n.45+25882C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9138 AN: 151530 Hom.: 617 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0518

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

GnomAD4 genome AF: 0.0603 AC: 9152 AN: 151656 Hom.: 619 Cov.: 32 AF XY: 0.0647 AC XY: 4794 AN XY: 74100

African (AFR) AF: 0.0440 AC: 1823 AN: 41454

American (AMR) AF: 0.165 AC: 2508 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3466

East Asian (EAS) AF: 0.310 AC: 1595 AN: 5148

South Asian (SAS) AF: 0.0813 AC: 392 AN: 4820

European-Finnish (FIN) AF: 0.0776 AC: 816 AN: 10514

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0273 AC: 1851 AN: 67758

Other (OTH) AF: 0.0527 AC: 111 AN: 2106

Alfa AF: 0.0387 Hom.: 458

Bravo AF: 0.0706

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.60
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2171325; hg19: chr2-78025576;