rs765728

Variant names:

• chr7-3113930-A-G
• rs765728
• ENST00000667422.1:n.75+4045T>C

Variant summary

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

The ENST00000667422.1(ENSG00000217455):​n.75+4045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,992 control chromosomes in the GnomAD database, including 15,799 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 0.45 (15799 hom., cov: 32)
• Consequence: ENSG00000217455 ENST00000667422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 1 publications found

Genes affected

ENSG00000217455 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667422.1. 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
	ENSG00000217455	ENST00000667422.1		n.75+4045T>C		intron	N/A
	ENSG00000217455	ENST00000703009.2		n.89+4045T>C		intron	N/A
	ENSG00000217455	ENST00000716171.1		n.248+6793T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68865 AN: 151874 Hom.: 15786 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.453 AC: 68910 AN: 151992 Hom.: 15799 Cov.: 32 AF XY: 0.451 AC XY: 33528 AN XY: 74292

African (AFR) AF: 0.402 AC: 16652 AN: 41442

American (AMR) AF: 0.447 AC: 6820 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2533 AN: 5166

South Asian (SAS) AF: 0.481 AC: 2312 AN: 4802

European-Finnish (FIN) AF: 0.409 AC: 4325 AN: 10574

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33269 AN: 67960

Other (OTH) AF: 0.439 AC: 928 AN: 2114

Alfa AF: 0.473 Hom.: 6118

Bravo AF: 0.449

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		0.0030

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: rs765728;

hg19: chr7-3153564;