rs1372679

Variant names:

• chr4-99383373-C-T
• rs1372679
• XR_001741777.2:n.635G>A

Variant summary

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

The XR_427569.4(LOC102723576):​n.1532G>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 0.0907 in 150,956 control chromosomes in the GnomAD database, including 717 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 0.091 (717 hom., cov: 28)
• Consequence: LOC102723576 XR_427569.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762194.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299279	ENST00000762194.1		n.506+119G>A		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.378+119G>A		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.621+119G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0908 AC: 13689 AN: 150840 Hom.: 714 Cov.: 28

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.0335

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0907 AC: 13698 AN: 150956 Hom.: 717 Cov.: 28 AF XY: 0.0934 AC XY: 6878 AN XY: 73650

African (AFR) AF: 0.0464 AC: 1911 AN: 41186

American (AMR) AF: 0.0942 AC: 1422 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.0335 AC: 116 AN: 3460

East Asian (EAS) AF: 0.144 AC: 716 AN: 4988

South Asian (SAS) AF: 0.0933 AC: 448 AN: 4800

European-Finnish (FIN) AF: 0.158 AC: 1634 AN: 10356

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7254 AN: 67774

Other (OTH) AF: 0.0745 AC: 156 AN: 2094

Alfa AF: 0.0983 Hom.: 463

Bravo AF: 0.0850

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.19
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1372679; hg19: chr4-100304530;