rs3896439

Variant names:

• chr1-4608610-G-A
• rs3896439
• ENST00000772751.1:n.1054G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-4608610-G-A
• chr1-4608610-G-C
• chr1-4608610-G-T

Variant summary

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

The ENST00000772751.1(ENSG00000300565):​n.1054G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 151,932 control chromosomes in the GnomAD database, including 1,044 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 0.095 (1044 hom., cov: 29)
• Consequence: ENSG00000300565 ENST00000772751.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 4 publications found

Genes affected

ENSG00000300565 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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
ENSG00000300565	ENST00000772751.1	n.1054G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000300565	ENST00000772752.1	n.1115G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000300565	ENST00000772748.1	n.482+567G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14475 AN: 151814 Hom.: 1038 Cov.: 29

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0901

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

GnomAD4 genome AF: 0.0955 AC: 14503 AN: 151932 Hom.: 1044 Cov.: 29 AF XY: 0.0971 AC XY: 7206 AN XY: 74232

African (AFR) AF: 0.169 AC: 7008 AN: 41410

American (AMR) AF: 0.0498 AC: 761 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1698 AN: 5118

South Asian (SAS) AF: 0.0799 AC: 384 AN: 4804

European-Finnish (FIN) AF: 0.0787 AC: 831 AN: 10554

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0480 AC: 3266 AN: 67992

Other (OTH) AF: 0.0939 AC: 198 AN: 2108

Alfa AF: 0.0658 Hom.: 2515

Bravo AF: 0.0955

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs3896439; hg19: chr1-4668670;