3-110582279-T-G

Position:

• chr3-110582279-T-G

Variant summary

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

The XR_924328.3(LOC105374037):​n.336-27330A>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 0.623 in 151,990 control chromosomes in the GnomAD database, including 29,633 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 0.62 (29633 hom., cov: 32)
• Consequence: LOC105374037 XR_924328.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

LOC105374037 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374037	XR_924328.3	n.336-27330A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94548 AN: 151872 Hom.: 29617 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.623 AC: 94618 AN: 151990 Hom.: 29633 Cov.: 32 AF XY: 0.624 AC XY: 46329 AN XY: 74270

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.629

Alfa AF: 0.641 Hom.: 15703

Bravo AF: 0.618

Asia WGS AF: 0.706 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2399332; hg19: chr3-110301126;