3-66703250-C-T

Position:

• chr3-66703250-C-T

Variant summary

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

The XR_940935.3(LOC105377142):​n.186-2065G>A 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 0.465 in 152,000 control chromosomes in the GnomAD database, including 17,449 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 0.46 (17449 hom., cov: 32)
• Consequence: LOC105377142 XR_940935.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

Genes affected

LOC105377142 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377142	XR_940935.3	n.186-2065G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70616 AN: 151882 Hom.: 17432 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.465 AC: 70670 AN: 152000 Hom.: 17449 Cov.: 32 AF XY: 0.463 AC XY: 34422 AN XY: 74280

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.449

Alfa AF: 0.397 Hom.: 14421

Bravo AF: 0.471

Asia WGS AF: 0.408 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11710109; hg19: chr3-66753674;