3-78006796-C-T

Position:

• chr3-78006796-C-T

Variant summary

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

The XR_940978.4(LOC105377171):​n.215+16005G>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 0.301 in 151,984 control chromosomes in the GnomAD database, including 7,318 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 0.30 (7318 hom., cov: 32)
• Consequence: LOC105377171 XR_940978.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

Genes affected

LOC105377171 (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 = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377171	XR_940978.4	n.215+16005G>A		intron_variant, non_coding_transcript_variant
LOC105377171	XR_940977.4	n.215+16005G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45799 AN: 151866 Hom.: 7308 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.301 AC: 45821 AN: 151984 Hom.: 7318 Cov.: 32 AF XY: 0.299 AC XY: 22186 AN XY: 74292

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.291

Alfa AF: 0.307 Hom.: 3427

Bravo AF: 0.294

Asia WGS AF: 0.336 AC: 1166 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	0.44
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7610746; hg19: chr3-78055947;