ENST00000771643.1:n.108+1816A>G

Variant names:

• chr3-485540-A-G
• rs6442890
• ENST00000771643.1:n.108+1816A>G

Variant summary

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

The ENST00000771643.1(ENSG00000300434):​n.108+1816A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,776 control chromosomes in the GnomAD database, including 19,043 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 0.50 (19043 hom., cov: 31)
• Consequence: ENSG00000300434 ENST00000771643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 3 publications found

Genes affected

ENSG00000300434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376922	XR_940538.2	n.346+1555A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300434	ENST00000771643.1	n.108+1816A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75119 AN: 151660 Hom.: 19010 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.495 AC: 75203 AN: 151776 Hom.: 19043 Cov.: 31 AF XY: 0.499 AC XY: 36992 AN XY: 74160

African (AFR) AF: 0.555 AC: 22960 AN: 41388

American (AMR) AF: 0.534 AC: 8151 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1751 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3682 AN: 5152

South Asian (SAS) AF: 0.498 AC: 2383 AN: 4782

European-Finnish (FIN) AF: 0.442 AC: 4638 AN: 10490

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30095 AN: 67920

Other (OTH) AF: 0.500 AC: 1055 AN: 2110

Alfa AF: 0.455 Hom.: 9865

Bravo AF: 0.505

Asia WGS AF: 0.577 AC: 2001 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.3
DANN	Benign	0.73
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs6442890; hg19: chr3-527223;