ENST00000782837.1:n.164+1194T>G

Variant names:

• chr2-175183178-T-G
• rs1982235
• ENST00000782837.1:n.164+1194T>G

Variant summary

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

The ENST00000782837.1(ENSG00000301915):​n.164+1194T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,190 control chromosomes in the GnomAD database, including 22,950 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 0.50 (22939 hom., cov: 33)
  • Exomes 𝑓: 0.66 (11 hom.)
• Consequence: ENSG00000301915 ENST00000782837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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+1194T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75558 AN: 152028 Hom.: 22929 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.529

GnomAD4 exome AF: 0.659 AC: 29 AN: 44 Hom.: 11 Cov.: 0 AF XY: 0.658 AC XY: 25 AN XY: 38

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.735 AC: 25 AN: 34

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.497 AC: 75580 AN: 152146 Hom.: 22939 Cov.: 33 AF XY: 0.501 AC XY: 37268 AN XY: 74394

African (AFR) AF: 0.138 AC: 5741 AN: 41504

American (AMR) AF: 0.486 AC: 7424 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2531 AN: 5170

South Asian (SAS) AF: 0.612 AC: 2954 AN: 4824

European-Finnish (FIN) AF: 0.733 AC: 7760 AN: 10580

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45322 AN: 67998

Other (OTH) AF: 0.532 AC: 1124 AN: 2114

Alfa AF: 0.601 Hom.: 90500

Bravo AF: 0.461

Asia WGS AF: 0.540 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.75
PhyloP100		0.87
Mutation Taster		=299/1	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: rs1982235; hg19: chr2-176047906;