7-86284446-T-C

Variant names:

• chr7-86284446-T-C
• rs2708553
• ENST00000757672.1:n.92+4322A>G

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.92+4322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 151,902 control chromosomes in the GnomAD database, including 42,661 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 0.74 (42661 hom., cov: 31)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 2 publications found

Genes affected

ENSG00000298738 (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 (SAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757672.1. 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
	ENSG00000298738	ENST00000757672.1		n.92+4322A>G		intron	N/A
	ENSG00000298738	ENST00000757673.1		n.91+4322A>G		intron	N/A
	ENSG00000298738	ENST00000757674.1		n.91+4322A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112430 AN: 151784 Hom.: 42622 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.741 AC: 112511 AN: 151902 Hom.: 42661 Cov.: 31 AF XY: 0.740 AC XY: 54964 AN XY: 74242

African (AFR) AF: 0.589 AC: 24425 AN: 41444

American (AMR) AF: 0.807 AC: 12303 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2989 AN: 3462

East Asian (EAS) AF: 0.924 AC: 4797 AN: 5194

South Asian (SAS) AF: 0.925 AC: 4472 AN: 4832

European-Finnish (FIN) AF: 0.648 AC: 6835 AN: 10550

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.798 AC: 54145 AN: 67856

Other (OTH) AF: 0.775 AC: 1634 AN: 2108

Alfa AF: 0.790 Hom.: 24336

Bravo AF: 0.742

Asia WGS AF: 0.896 AC: 3104 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.1
DANN	Benign	0.67
PhyloP100		1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2708553;

hg19: chr7-85913762;