chr2-226136270-G-A

Variant names:

• chr2-226136270-G-A
• rs6758183
• ENST00000719962.1:n.94-48235C>T

Variant summary

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

The ENST00000719962.1(ENSG00000235070):​n.94-48235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,172 control chromosomes in the GnomAD database, including 3,228 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 0.19 (3228 hom., cov: 33)
• Consequence: ENSG00000235070 ENST00000719962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 11 publications found

Genes affected

ENSG00000235070 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235070	ENST00000719962.1	n.94-48235C>T		intron_variant	Intron 1 of 1
ENSG00000235070	ENST00000719963.1	n.143+7698C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29160 AN: 152054 Hom.: 3231 Cov.: 33

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.192 AC: 29153 AN: 152172 Hom.: 3228 Cov.: 33 AF XY: 0.187 AC XY: 13913 AN XY: 74408

African (AFR) AF: 0.0954 AC: 3962 AN: 41530

American (AMR) AF: 0.182 AC: 2781 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3472

East Asian (EAS) AF: 0.0707 AC: 366 AN: 5176

South Asian (SAS) AF: 0.241 AC: 1166 AN: 4832

European-Finnish (FIN) AF: 0.174 AC: 1848 AN: 10596

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17269 AN: 67968

Other (OTH) AF: 0.239 AC: 504 AN: 2108

Alfa AF: 0.232 Hom.: 14458

Bravo AF: 0.186

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6758183; hg19: chr2-227000986;