3-66965486-T-G

Position:

• chr3-66965486-T-G

Variant summary

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

The XR_940939.2(LOC105377144):​n.74+6859A>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 0.781 in 152,080 control chromosomes in the GnomAD database, including 46,660 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 0.78 (46660 hom., cov: 31)
• Consequence: LOC105377144 XR_940939.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

Genes affected

LOC105377144 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377144	XR_940939.2	n.74+6859A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118666 AN: 151962 Hom.: 46614 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.781 AC: 118771 AN: 152080 Hom.: 46660 Cov.: 31 AF XY: 0.785 AC XY: 58332 AN XY: 74334

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.771

Alfa AF: 0.790 Hom.: 59170

Bravo AF: 0.778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6807497; hg19: chr3-67015910;