rs130058

chr6-77463564-T-Achr6-77463564-T-Cchr6-77463564-T-G

Variant summary

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

The XM_047419660.1(LOC105377864):c.-3742-10962T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 673,436 control chromosomes in the GnomAD database, including 26,820 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 0.23 (5071 hom., cov: 32)
  • Exomes 𝑓: 0.28 (21749 hom.)
• Consequence: LOC105377864 XM_047419660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377864	XM_047419660.1	c.-3742-10962T>A		intron_variant
LOC105377864	XM_047419659.1	c.-10895T>A		5_prime_UTR_variant	2/6
LOC105377864	XM_047419661.1	c.-3917+446T>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35268 AN: 151876 Hom.: 5069 Cov.: 32

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.267

GnomAD4 exome AF: 0.278 AC: 145206 AN: 521440 Hom.: 21749 Cov.: 6 AF XY: 0.278 AC XY: 75293 AN XY: 271252

Gnomad4 AFR exome AF: 0.0654

Gnomad4 AMR exome AF: 0.296

Gnomad4 ASJ exome AF: 0.328

Gnomad4 EAS exome AF: 0.0732

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.361

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.279

GnomAD4 genome AF: 0.232 AC: 35280 AN: 151996 Hom.: 5071 Cov.: 32 AF XY: 0.235 AC XY: 17495 AN XY: 74296

Gnomad4 AFR AF: 0.0702

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.0934

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.266

Alfa AF: 0.143 Hom.: 280

Bravo AF: 0.220

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	13
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs130058; hg19: chr6-78173281; COSMIC: COSV64052002;