4-45971222-G-A

Variant names:

• chr4-45971222-G-A
• rs1394344
• ENST00000794649.1:n.182-1381C>T

Variant summary

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

The ENST00000794649.1(ENSG00000303444):​n.182-1381C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,816 control chromosomes in the GnomAD database, including 18,446 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 0.48 (18446 hom., cov: 31)
• Consequence: ENSG00000303444 ENST00000794649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 4 publications found

Genes affected

ENSG00000303444 (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 = 0.63 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
ENSG00000303444	ENST00000794649.1	n.182-1381C>T		intron_variant	Intron 1 of 3
ENSG00000303444	ENST00000794650.1	n.119-1381C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73079 AN: 151698 Hom.: 18406 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.482 AC: 73193 AN: 151816 Hom.: 18446 Cov.: 31 AF XY: 0.477 AC XY: 35344 AN XY: 74172

African (AFR) AF: 0.636 AC: 26338 AN: 41388

American (AMR) AF: 0.458 AC: 6980 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1419 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1672 AN: 5138

South Asian (SAS) AF: 0.263 AC: 1266 AN: 4820

European-Finnish (FIN) AF: 0.447 AC: 4708 AN: 10542

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29276 AN: 67922

Other (OTH) AF: 0.451 AC: 949 AN: 2102

Alfa AF: 0.460 Hom.: 2056

Bravo AF: 0.493

Asia WGS AF: 0.334 AC: 1162 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	1.4
DANN	Benign	0.32
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1394344; hg19: chr4-45973239;