3-72599829-A-G

Position:

• chr3-72599829-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_940962.3(LOC105377161):​n.1153+1732T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,068 control chromosomes in the GnomAD database, including 2,155 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 0.16 (2155 hom., cov: 32)
• Consequence: LOC105377161 XR_940962.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55

Genes affected

LOC105377161 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377161	XR_940962.3	n.1153+1732T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24203 AN: 151950 Hom.: 2148 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.159 AC: 24227 AN: 152068 Hom.: 2155 Cov.: 32 AF XY: 0.162 AC XY: 12068 AN XY: 74326

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.185

Alfa AF: 0.139 Hom.: 2135

Bravo AF: 0.169

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.084
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10049135; hg19: chr3-72648980;