rs4859365

Variant names:

• chr4-35520910-G-A
• rs4859365
• ENST00000743803.1:n.385-1467G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-35520910-G-A
• chr4-35520910-G-C
• chr4-35520910-G-T

Variant summary

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

The ENST00000743803.1(ENSG00000296945):​n.385-1467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,590 control chromosomes in the GnomAD database, including 21,333 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 0.53 (21333 hom., cov: 32)
• Consequence: ENSG00000296945 ENST00000743803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 1 publications found

Genes affected

ENSG00000296945 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743803.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296945	ENST00000743803.1		n.385-1467G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 79986 AN: 151472 Hom.: 21305 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.528 AC: 80045 AN: 151590 Hom.: 21333 Cov.: 32 AF XY: 0.524 AC XY: 38817 AN XY: 74038

African (AFR) AF: 0.585 AC: 24156 AN: 41304

American (AMR) AF: 0.465 AC: 7088 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3470

East Asian (EAS) AF: 0.714 AC: 3676 AN: 5150

South Asian (SAS) AF: 0.413 AC: 1985 AN: 4806

European-Finnish (FIN) AF: 0.483 AC: 5046 AN: 10444

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34522 AN: 67866

Other (OTH) AF: 0.523 AC: 1104 AN: 2110

Alfa AF: 0.525 Hom.: 2640

Bravo AF: 0.536

Asia WGS AF: 0.540 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.073
DANN	Benign	0.82
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4859365; hg19: chr4-35522532;