4-99382001-G-C

Variant names:

• chr4-99382001-G-C
• rs10516439
• XR_001741777.2:n.2007C>G

Variant summary

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

The XR_001741777.2(LOC102723576):​n.2007C>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 0.254 in 152,126 control chromosomes in the GnomAD database, including 5,739 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 0.25 (5739 hom., cov: 33)
• Consequence: LOC102723576 XR_001741777.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.2007C>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC102723576	XR_427569.4	n.2904C>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC102723576	XR_939020.3	n.1413+1491C>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.506+1491C>G		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762195.1	n.378+1491C>G		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762196.1	n.621+1491C>G		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762198.1	n.233+1491C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38549 AN: 152008 Hom.: 5732 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.254 AC: 38584 AN: 152126 Hom.: 5739 Cov.: 33 AF XY: 0.260 AC XY: 19358 AN XY: 74382

African (AFR) AF: 0.320 AC: 13284 AN: 41498

American (AMR) AF: 0.183 AC: 2797 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3487 AN: 5164

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4818

European-Finnish (FIN) AF: 0.172 AC: 1828 AN: 10600

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13535 AN: 67978

Other (OTH) AF: 0.237 AC: 500 AN: 2110

Alfa AF: 0.214 Hom.: 481

Bravo AF: 0.254

Asia WGS AF: 0.468 AC: 1625 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.39
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10516439; hg19: chr4-100303158;