rs1213368

Variant names:

• chr6-77468413-A-G
• rs1213368
• XM_047419658.1:c.-6220A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047419658.1(LOC105377864):​c.-6220A>G variant causes a 5 prime UTR premature start codon gain 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_047419658.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 3 publications found

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105377864	XM_047419658.1	c.-6220A>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 6		XP_047275614.1
LOC105377864	XM_047419659.1	c.-6046A>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 6		XP_047275615.1
LOC105377864	XM_047419658.1	c.-6220A>G		5_prime_UTR_variant	Exon 1 of 6		XP_047275614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296750	ENST00000741553.1	n.231+1597A>G		intron_variant	Intron 1 of 3
ENSG00000296750	ENST00000741554.1	n.124+1593A>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.421 AC: 17447 AN: 41446

American (AMR) AF: 0.451 AC: 6901 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3468

East Asian (EAS) AF: 0.620 AC: 3199 AN: 5156

South Asian (SAS) AF: 0.393 AC: 1897 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3264 AN: 10568

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20714 AN: 67942

Other (OTH) AF: 0.364 AC: 768 AN: 2110

Alfa AF: 0.335 Hom.: 2383

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
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1213368; hg19: chr6-78178130;