rs7578326

Variant names:

• chr2-226155937-A-G
• rs7578326
• ENST00000719962.1:n.93+29383T>C

Variant summary

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

The ENST00000719962.1(ENSG00000235070):​n.93+29383T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,988 control chromosomes in the GnomAD database, including 9,678 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 0.35 (9678 hom., cov: 32)
• Consequence: ENSG00000235070 ENST00000719962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 130 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC646736	NR_046102.1	n.293-8451A>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235070	ENST00000719962.1	n.93+29383T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53449 AN: 151870 Hom.: 9660 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.352 AC: 53499 AN: 151988 Hom.: 9678 Cov.: 32 AF XY: 0.350 AC XY: 26000 AN XY: 74274

African (AFR) AF: 0.414 AC: 17159 AN: 41464

American (AMR) AF: 0.311 AC: 4752 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 994 AN: 3468

East Asian (EAS) AF: 0.155 AC: 802 AN: 5160

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4816

European-Finnish (FIN) AF: 0.352 AC: 3706 AN: 10540

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23934 AN: 67958

Other (OTH) AF: 0.343 AC: 724 AN: 2110

Alfa AF: 0.347 Hom.: 37292

Bravo AF: 0.351

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7578326; hg19: chr2-227020653;