rs11568817

chr6-77463665-A-C

Variant summary

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

The XM_047419660.1(LOC105377864):c.-3742-10861A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 565,208 control chromosomes in the GnomAD database, including 50,950 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 0.37 (11621 hom., cov: 32)
  • Exomes 𝑓: 0.42 (39329 hom.)
• Consequence: LOC105377864 XM_047419660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377864	XM_047419660.1	c.-3742-10861A>C		intron_variant
LOC105377864	XM_047419659.1	c.-10794A>C		5_prime_UTR_variant	2/6
LOC105377864	XM_047419661.1	c.-3917+547A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55967 AN: 151784 Hom.: 11621 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.417

GnomAD4 exome AF: 0.423 AC: 174763 AN: 413304 Hom.: 39329 Cov.: 2 AF XY: 0.427 AC XY: 92270 AN XY: 216340

Gnomad4 AFR exome AF: 0.193

Gnomad4 AMR exome AF: 0.394

Gnomad4 ASJ exome AF: 0.541

Gnomad4 EAS exome AF: 0.104

Gnomad4 SAS exome AF: 0.464

Gnomad4 FIN exome AF: 0.463

Gnomad4 NFE exome AF: 0.454

Gnomad4 OTH exome AF: 0.429

GnomAD4 genome AF: 0.369 AC: 56005 AN: 151904 Hom.: 11621 Cov.: 32 AF XY: 0.371 AC XY: 27544 AN XY: 74224

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.414

Alfa AF: 0.397 Hom.: 1661

Bravo AF: 0.354

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.7
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11568817; hg19: chr6-78173382;