chr7-3113930-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375130	XR_007060191.1	n.60+4045T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000217455	ENST00000667422.1	n.75+4045T>C		intron_variant	Intron 1 of 1
ENSG00000217455	ENST00000703009.2	n.89+4045T>C		intron_variant	Intron 1 of 1
ENSG00000217455	ENST00000716171.1	n.248+6793T>C		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs765728; hg19: chr7-3153564;