rs7694379

Variant names:

• chr4-87265357-G-A
• rs7694379
• ENST00000503666.2:n.438+1378C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-87265357-G-A
• chr4-87265357-G-C

Variant summary

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

The ENST00000503666.2(ENSG00000250572):​n.438+1378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,030 control chromosomes in the GnomAD database, including 12,180 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 0.40 (12180 hom., cov: 32)
• Consequence: ENSG00000250572 ENST00000503666.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 21 publications found

Genes affected

ENSG00000250572 (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 (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503666.2. 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
	ENSG00000250572	ENST00000503666.2	TSL:2	n.438+1378C>T		intron	N/A
	ENSG00000250572	ENST00000729938.1		n.407-643C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60396 AN: 151912 Hom.: 12174 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.397 AC: 60425 AN: 152030 Hom.: 12180 Cov.: 32 AF XY: 0.388 AC XY: 28795 AN XY: 74302

African (AFR) AF: 0.432 AC: 17909 AN: 41428

American (AMR) AF: 0.337 AC: 5147 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1438 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1893 AN: 5170

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4818

European-Finnish (FIN) AF: 0.326 AC: 3453 AN: 10582

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28290 AN: 67962

Other (OTH) AF: 0.385 AC: 814 AN: 2112

Alfa AF: 0.412 Hom.: 26307

Bravo AF: 0.404

Asia WGS AF: 0.299 AC: 1041 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs7694379; hg19: chr4-88186509;