3-66909048-T-C

Position:

• chr3-66909048-T-C

Variant summary

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

The XR_940939.2(LOC105377144):​n.75-29454A>G 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 0.722 in 152,092 control chromosomes in the GnomAD database, including 40,605 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 0.72 (40605 hom., cov: 32)
• Consequence: LOC105377144 XR_940939.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

LOC105377144 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377144	XR_940939.2	n.75-29454A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109721 AN: 151974 Hom.: 40582 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.722 AC: 109787 AN: 152092 Hom.: 40605 Cov.: 32 AF XY: 0.728 AC XY: 54140 AN XY: 74356

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.718

Alfa AF: 0.753 Hom.: 40409

Bravo AF: 0.713

Asia WGS AF: 0.883 AC: 3068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456217; hg19: chr3-66959472;