2-76378967-G-T

Variant names:

• chr2-76378967-G-T
• rs908959
• ENST00000654219.1:n.191-6263G>T

Variant summary

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

The ENST00000654219.1(ENSG00000287172):​n.191-6263G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,094 control chromosomes in the GnomAD database, including 48,277 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 (48277 hom., cov: 32)
• Consequence: ENSG00000287172 ENST00000654219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 3 publications found

Genes affected

ENSG00000287172 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654219.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287172	ENST00000654219.1		n.191-6263G>T		intron	N/A
	ENSG00000287172	ENST00000668214.1		n.163-16721G>T		intron	N/A
	ENSG00000287172	ENST00000669228.1		n.191-6285G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120261 AN: 151976 Hom.: 48258 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.791 AC: 120325 AN: 152094 Hom.: 48277 Cov.: 32 AF XY: 0.789 AC XY: 58675 AN XY: 74358

African (AFR) AF: 0.673 AC: 27901 AN: 41458

American (AMR) AF: 0.742 AC: 11347 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3132 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3507 AN: 5158

South Asian (SAS) AF: 0.810 AC: 3901 AN: 4814

European-Finnish (FIN) AF: 0.813 AC: 8613 AN: 10588

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59239 AN: 67996

Other (OTH) AF: 0.810 AC: 1715 AN: 2116

Alfa AF: 0.840 Hom.: 143860

Bravo AF: 0.778

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.42
PhyloP100		1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs908959;

hg19: chr2-76606093;