chr4-99382344-G-T

Variant names:

• chr4-99382344-G-T
• rs2851292
• XR_001741777.2:n.1664C>A

Variant summary

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

The XR_001741777.2(LOC102723576):​n.1664C>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 0.883 in 152,158 control chromosomes in the GnomAD database, including 59,475 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 0.88 (59475 hom., cov: 32)
• Consequence: LOC102723576 XR_001741777.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.916 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+1148C>A		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.378+1148C>A		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.621+1148C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134205 AN: 152040 Hom.: 59428 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.883 AC: 134313 AN: 152158 Hom.: 59475 Cov.: 32 AF XY: 0.882 AC XY: 65592 AN XY: 74366

African (AFR) AF: 0.924 AC: 38384 AN: 41540

American (AMR) AF: 0.829 AC: 12641 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2621 AN: 3472

East Asian (EAS) AF: 0.855 AC: 4433 AN: 5182

South Asian (SAS) AF: 0.934 AC: 4508 AN: 4824

European-Finnish (FIN) AF: 0.855 AC: 9041 AN: 10572

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.880 AC: 59857 AN: 68002

Other (OTH) AF: 0.849 AC: 1788 AN: 2106

Alfa AF: 0.889 Hom.: 7803

Bravo AF: 0.877

Asia WGS AF: 0.833 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2851292; hg19: chr4-100303501;