7-25332081-C-T

Variant names:

• chr7-25332081-C-T
• rs4722456
• ENST00000718235.1:n.399-6675G>A

Variant summary

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

The ENST00000718235.1(ENSG00000233824):​n.399-6675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,072 control chromosomes in the GnomAD database, including 13,454 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 0.41 (13454 hom., cov: 33)
• Consequence: ENSG00000233824 ENST00000718235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 4 publications found

Genes affected

ENSG00000233824 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375195	XR_927105.2	n.890+616C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233824	ENST00000718235.1	n.399-6675G>A		intron_variant	Intron 2 of 3
ENSG00000233824	ENST00000765804.1	n.381-5221G>A		intron_variant	Intron 2 of 2
ENSG00000299736	ENST00000765944.1	n.170+616C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61939 AN: 151954 Hom.: 13453 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.407 AC: 61953 AN: 152072 Hom.: 13454 Cov.: 33 AF XY: 0.407 AC XY: 30270 AN XY: 74344

African (AFR) AF: 0.254 AC: 10521 AN: 41486

American (AMR) AF: 0.406 AC: 6203 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2607 AN: 5162

South Asian (SAS) AF: 0.383 AC: 1841 AN: 4810

European-Finnish (FIN) AF: 0.442 AC: 4672 AN: 10572

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32798 AN: 67970

Other (OTH) AF: 0.448 AC: 947 AN: 2112

Alfa AF: 0.459 Hom.: 12256

Bravo AF: 0.402

Asia WGS AF: 0.428 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.93
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4722456; hg19: chr7-25371700;