chr2-135728087-C-T

Variant names:

• chr2-135728087-C-T
• rs1347767
• ENST00000836082.1:n.93+13528G>A

Variant summary

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

The ENST00000836082.1(ENSG00000308733):​n.93+13528G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.973 in 152,252 control chromosomes in the GnomAD database, including 72,154 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 0.97 (72154 hom., cov: 33)
• Consequence: ENSG00000308733 ENST00000836082.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 3 publications found

Genes affected

ENSG00000308733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836082.1. 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
	ENSG00000308733	ENST00000836082.1		n.93+13528G>A		intron	N/A
	ENSG00000308733	ENST00000836083.1		n.81+13528G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.973 AC: 147991 AN: 152134 Hom.: 72104 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.966

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.982

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

GnomAD4 genome AF: 0.973 AC: 148100 AN: 152252 Hom.: 72154 Cov.: 33 AF XY: 0.972 AC XY: 72368 AN XY: 74436

African (AFR) AF: 0.913 AC: 37935 AN: 41562

American (AMR) AF: 0.987 AC: 15103 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3454 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5081 AN: 5170

South Asian (SAS) AF: 0.966 AC: 4661 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10600 AN: 10600

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67994 AN: 68012

Other (OTH) AF: 0.982 AC: 2068 AN: 2106

Alfa AF: 0.986 Hom.: 15001

Bravo AF: 0.970

Asia WGS AF: 0.962 AC: 3348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1347767; hg19: chr2-136485657;