chr7-45388930-A-G

Variant names:

• chr7-45388930-A-G
• rs1122780
• ENST00000847203.1:n.406+4128A>G

Variant summary

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

The ENST00000847203.1(ENSG00000286738):​n.406+4128A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,150 control chromosomes in the GnomAD database, including 6,172 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 0.28 (6172 hom., cov: 32)
• Consequence: ENSG00000286738 ENST00000847203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 4 publications found

Genes affected

ENSG00000286738 (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 = 0.372 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
ENSG00000286738	ENST00000847203.1	n.406+4128A>G		intron_variant	Intron 3 of 3
ENSG00000286738	ENST00000847204.1	n.315+4128A>G		intron_variant	Intron 2 of 2
ENSG00000286738	ENST00000847205.1	n.122+4128A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42298 AN: 152032 Hom.: 6164 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.278 AC: 42348 AN: 152150 Hom.: 6172 Cov.: 32 AF XY: 0.276 AC XY: 20532 AN XY: 74370

African (AFR) AF: 0.377 AC: 15638 AN: 41494

American (AMR) AF: 0.240 AC: 3666 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3472

East Asian (EAS) AF: 0.111 AC: 575 AN: 5192

South Asian (SAS) AF: 0.188 AC: 907 AN: 4818

European-Finnish (FIN) AF: 0.268 AC: 2832 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17007 AN: 67996

Other (OTH) AF: 0.275 AC: 582 AN: 2116

Alfa AF: 0.273 Hom.: 2103

Bravo AF: 0.283

Asia WGS AF: 0.193 AC: 668 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.71
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1122780; hg19: chr7-45428529;