ENST00000782837.1:n.164+150C>A

Variant names:

• chr2-175182134-C-A
• rs268230
• ENST00000782837.1:n.164+150C>A

Variant summary

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

The ENST00000782837.1(ENSG00000301915):​n.164+150C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,100 control chromosomes in the GnomAD database, including 43,754 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 0.75 (43738 hom., cov: 31)
  • Exomes 𝑓: 0.86 (16 hom.)
• Consequence: ENSG00000301915 ENST00000782837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 12 publications found

Genes affected

ENSG00000301915 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782837.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301915	ENST00000782837.1		n.164+150C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114322 AN: 151940 Hom.: 43710 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.744

GnomAD4 exome AF: 0.857 AC: 36 AN: 42 Hom.: 16 Cov.: 0 AF XY: 0.861 AC XY: 31 AN XY: 36

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.958 AC: 23 AN: 24

Other (OTH) AF: 0.500 AC: 3 AN: 6

GnomAD4 genome AF: 0.752 AC: 114391 AN: 152058 Hom.: 43738 Cov.: 31 AF XY: 0.756 AC XY: 56209 AN XY: 74326

African (AFR) AF: 0.594 AC: 24601 AN: 41430

American (AMR) AF: 0.745 AC: 11390 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2658 AN: 3472

East Asian (EAS) AF: 0.862 AC: 4446 AN: 5158

South Asian (SAS) AF: 0.809 AC: 3899 AN: 4820

European-Finnish (FIN) AF: 0.883 AC: 9350 AN: 10584

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55456 AN: 67994

Other (OTH) AF: 0.747 AC: 1576 AN: 2110

Alfa AF: 0.762 Hom.: 6758

Bravo AF: 0.732

Asia WGS AF: 0.818 AC: 2844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.27
DANN	Benign	0.81
PhyloP100		-1.5
PromoterAI		-0.073	Neutral
Mutation Taster		=298/2	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs268230; hg19: chr2-176046862;