3-45315935-G-A

Variant names:

• chr3-45315935-G-A
• rs9850725
• ENST00000756647.1:n.34+3648G>A

Variant summary

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

The ENST00000756647.1(ENSG00000298579):​n.34+3648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,204 control chromosomes in the GnomAD database, including 691 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 0.056 (691 hom., cov: 32)
• Consequence: ENSG00000298579 ENST00000756647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 1 publications found

Genes affected

ENSG00000298579 (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 (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377061	XR_001740678.1	n.980+5784G>A		intron_variant	Intron 2 of 2
LOC105377061	XR_001740679.1	n.980+5784G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298579	ENST00000756647.1	n.34+3648G>A		intron_variant	Intron 1 of 1
ENSG00000298579	ENST00000756648.1	n.46+3648G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8497 AN: 152086 Hom.: 684 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0562 AC: 8549 AN: 152204 Hom.: 691 Cov.: 32 AF XY: 0.0558 AC XY: 4152 AN XY: 74426

African (AFR) AF: 0.179 AC: 7421 AN: 41484

American (AMR) AF: 0.0234 AC: 358 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3472

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5180

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10606

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00237 AC: 161 AN: 68024

Other (OTH) AF: 0.0417 AC: 88 AN: 2112

Alfa AF: 0.0251 Hom.: 81

Bravo AF: 0.0624

Asia WGS AF: 0.0590 AC: 207 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	5.6
DANN	Benign	0.78
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs9850725; hg19: chr3-45357427;