rs1372680

Variant names:

• chr4-99383388-C-A
• rs1372680
• XR_001741777.2:n.620G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-99383388-C-A
• chr4-99383388-C-T

Variant summary

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

The XR_001741777.2(LOC102723576):​n.620G>T 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 0.0995 in 150,788 control chromosomes in the GnomAD database, including 814 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 0.099 (814 hom., cov: 28)
• Consequence: LOC102723576 XR_001741777.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299279	ENST00000762194.1		n.506+104G>T		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.378+104G>T		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.621+104G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 14989 AN: 150670 Hom.: 810 Cov.: 28

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0995 AC: 15003 AN: 150788 Hom.: 814 Cov.: 28 AF XY: 0.102 AC XY: 7502 AN XY: 73542

African (AFR) AF: 0.0717 AC: 2946 AN: 41094

American (AMR) AF: 0.104 AC: 1567 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3464

East Asian (EAS) AF: 0.142 AC: 707 AN: 4974

South Asian (SAS) AF: 0.0943 AC: 450 AN: 4774

European-Finnish (FIN) AF: 0.157 AC: 1617 AN: 10312

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7363 AN: 67772

Other (OTH) AF: 0.0880 AC: 185 AN: 2102

Alfa AF: 0.0948 Hom.: 1293

Bravo AF: 0.0952

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs1372680; hg19: chr4-100304545;