7-51661984-A-T

Variant names:

• chr7-51661984-A-T
• rs7791504
• ENST00000648455.1:n.353-2724A>T

Variant summary

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

The ENST00000648455.1(ENSG00000285741):​n.353-2724A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,094 control chromosomes in the GnomAD database, including 31,341 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 0.64 (31341 hom., cov: 32)
• Consequence: ENSG00000285741 ENST00000648455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 1 publications found

Genes affected

ENSG00000285741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648455.1. 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
	ENSG00000285741	ENST00000648455.1		n.353-2724A>T		intron	N/A
	ENSG00000285741	ENST00000769890.1		n.481-2724A>T		intron	N/A
	ENSG00000285741	ENST00000769891.1		n.470-2724A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97066 AN: 151974 Hom.: 31307 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.639 AC: 97156 AN: 152094 Hom.: 31341 Cov.: 32 AF XY: 0.634 AC XY: 47150 AN XY: 74344

African (AFR) AF: 0.729 AC: 30258 AN: 41496

American (AMR) AF: 0.595 AC: 9098 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3472

East Asian (EAS) AF: 0.642 AC: 3291 AN: 5130

South Asian (SAS) AF: 0.617 AC: 2976 AN: 4820

European-Finnish (FIN) AF: 0.572 AC: 6053 AN: 10586

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41404 AN: 67986

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.516 Hom.: 1378

Bravo AF: 0.645

Asia WGS AF: 0.614 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.63
PhyloP100		-0.76

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: rs7791504;

hg19: chr7-51729680;