rs989631

Positions:

• chr4-23044899-G-A
• chr4-23044899-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663348.1(ENSG00000248837):​n.169-38798G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,880 control chromosomes in the GnomAD database, including 7,804 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 0.30 (7804 hom., cov: 32)
• Consequence: ENST00000663348.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374524	XR_007058434.1	n.305-38798G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663348.1	n.169-38798G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45074 AN: 151762 Hom.: 7794 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.297 AC: 45123 AN: 151880 Hom.: 7804 Cov.: 32 AF XY: 0.301 AC XY: 22328 AN XY: 74250

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.282

Alfa AF: 0.136 Hom.: 222

Bravo AF: 0.320

Asia WGS AF: 0.484 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs989631; hg19: chr4-23046522;