ENST00000671393.1:n.295-10377G>A

Variant names:

• chr2-184322417-G-A
• rs719736
• ENST00000671393.1:n.295-10377G>A

Variant summary

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

The ENST00000671393.1(ENSG00000286980):​n.295-10377G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,988 control chromosomes in the GnomAD database, including 14,816 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 0.40 (14816 hom., cov: 32)
• Consequence: ENSG00000286980 ENST00000671393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 5 publications found

Genes affected

ENSG00000286980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724340	XR_001739818.2	n.133-10377G>A		intron_variant	Intron 2 of 3
LOC102724340	XR_001739819.1	n.219-10377G>A		intron_variant	Intron 2 of 4
LOC105373776	XR_923650.3	n.192-30413C>T		intron_variant	Intron 2 of 3
LOC102724340	XR_923652.2	n.219-10377G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286980	ENST00000671393.1	n.295-10377G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60796 AN: 151870 Hom.: 14804 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.400 AC: 60806 AN: 151988 Hom.: 14816 Cov.: 32 AF XY: 0.401 AC XY: 29777 AN XY: 74246

African (AFR) AF: 0.105 AC: 4357 AN: 41484

American (AMR) AF: 0.536 AC: 8175 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2065 AN: 3462

East Asian (EAS) AF: 0.466 AC: 2401 AN: 5150

South Asian (SAS) AF: 0.481 AC: 2316 AN: 4814

European-Finnish (FIN) AF: 0.501 AC: 5286 AN: 10544

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34842 AN: 67966

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.490 Hom.: 32829

Bravo AF: 0.391

Asia WGS AF: 0.480 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs719736; hg19: chr2-185187144;