7-57316046-A-T

Variant names:

• chr7-57316046-A-T
• rs7808342
• ENST00000824795.1:n.230+10353A>T

Variant summary

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

The ENST00000824795.1(ENSG00000307257):​n.230+10353A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,114 control chromosomes in the GnomAD database, including 53,316 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 0.83 (53316 hom., cov: 32)
• Consequence: ENSG00000307257 ENST00000824795.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 1 publications found

Genes affected

ENSG00000307257 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 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
ENSG00000307257	ENST00000824795.1	n.230+10353A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126682 AN: 151996 Hom.: 53256 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.834 AC: 126803 AN: 152114 Hom.: 53316 Cov.: 32 AF XY: 0.837 AC XY: 62213 AN XY: 74370

African (AFR) AF: 0.928 AC: 38509 AN: 41518

American (AMR) AF: 0.845 AC: 12896 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2336 AN: 3468

East Asian (EAS) AF: 0.913 AC: 4708 AN: 5156

South Asian (SAS) AF: 0.864 AC: 4159 AN: 4814

European-Finnish (FIN) AF: 0.827 AC: 8753 AN: 10580

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52832 AN: 67998

Other (OTH) AF: 0.781 AC: 1644 AN: 2104

Alfa AF: 0.751 Hom.: 2257

Bravo AF: 0.839

Asia WGS AF: 0.848 AC: 2950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.75
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7808342; hg19: chr7-57383753;