4-99379891-T-C

Variant names:

• chr4-99379891-T-C
• rs1826906
• XR_427569.4:n.5014A>G

Variant summary

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

The XR_427569.4(LOC102723576):​n.5014A>G 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 0.377 in 151,760 control chromosomes in the GnomAD database, including 11,569 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 0.38 (11569 hom., cov: 31)
• Consequence: LOC102723576 XR_427569.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 4 publications found

Genes affected

LOC102723576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_427569.4	n.5014A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC102723576	XR_939020.3	n.1414-999A>G		intron_variant	Intron 4 of 4
LOC102723576	XR_001741777.2	n.*174A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.507-999A>G		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762195.1	n.379-999A>G		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762196.1	n.622-999A>G		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762198.1	n.234-999A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57080 AN: 151642 Hom.: 11546 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.377 AC: 57148 AN: 151760 Hom.: 11569 Cov.: 31 AF XY: 0.386 AC XY: 28583 AN XY: 74134

African (AFR) AF: 0.433 AC: 17934 AN: 41396

American (AMR) AF: 0.310 AC: 4726 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3466

East Asian (EAS) AF: 0.818 AC: 4224 AN: 5164

South Asian (SAS) AF: 0.570 AC: 2739 AN: 4808

European-Finnish (FIN) AF: 0.332 AC: 3487 AN: 10500

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22170 AN: 67874

Other (OTH) AF: 0.350 AC: 738 AN: 2108

Alfa AF: 0.338 Hom.: 38490

Bravo AF: 0.374

Asia WGS AF: 0.599 AC: 2081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1826906; hg19: chr4-100301048;