rs1004689

Positions:

• chr22-48256185-T-G

Variant summary

Our verdict is Benign. Variant got -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: ENST00000648313.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648313.1	n.1234A>C		non_coding_transcript_exon_variant	3/3

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

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.454

Alfa AF: 0.351 Hom.: 13159

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1004689; hg19: chr22-48651997;