rs1004689

Variant names:

• chr22-48256185-T-G
• rs1004689
• ENST00000648313.1:n.1234A>C

Variant summary

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

The ENST00000648313.1(ENSG00000285707):​n.1234A>C 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 0.471 in 152,060 control chromosomes in the GnomAD database, including 19,871 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 0.47 (19871 hom., cov: 32)
• Consequence: ENSG00000285707 ENST00000648313.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 3 publications found

Genes affected

ENSG00000285707 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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
ENSG00000285707	ENST00000648313.1	n.1234A>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71454 AN: 151940 Hom.: 19819 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.471 AC: 71563 AN: 152060 Hom.: 19871 Cov.: 32 AF XY: 0.467 AC XY: 34694 AN XY: 74310

African (AFR) AF: 0.775 AC: 32123 AN: 41468

American (AMR) AF: 0.397 AC: 6067 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2830 AN: 5148

South Asian (SAS) AF: 0.374 AC: 1806 AN: 4824

European-Finnish (FIN) AF: 0.324 AC: 3425 AN: 10566

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22614 AN: 67990

Other (OTH) AF: 0.454 AC: 958 AN: 2108

Alfa AF: 0.370 Hom.: 21007

Bravo AF: 0.488

Asia WGS AF: 0.474 AC: 1651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1004689; hg19: chr22-48651997;