rs1213368

Positions:

• chr6-77468413-A-G

Variant summary

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

The XM_047419660.1(LOC105377864):​c.-3742-6113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,008 control chromosomes in the GnomAD database, including 10,762 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 (10762 hom., cov: 32)
• Consequence: LOC105377864 XM_047419660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

Genes affected

LOC105377864 (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 = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377864	XM_047419660.1	c.-3742-6113A>G		intron_variant
LOC105377864	XM_047419658.1	c.-6220A>G		5_prime_UTR_variant	1/6
LOC105377864	XM_047419659.1	c.-6046A>G		5_prime_UTR_variant	2/6
LOC105377864	XM_047419661.1	c.-3917+5295A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55697 AN: 151890 Hom.: 10763 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.367 AC: 55717 AN: 152008 Hom.: 10762 Cov.: 32 AF XY: 0.371 AC XY: 27568 AN XY: 74330

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.364

Alfa AF: 0.339 Hom.: 1182

Bravo AF: 0.383

Asia WGS AF: 0.504 AC: 1746 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1213368; hg19: chr6-78178130;