rs6894385

Positions:

• chr5-73981078-A-C

Variant summary

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

The XR_001742745.1(LOC105379034):​n.1598-1287A>C 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 0.158 in 152,082 control chromosomes in the GnomAD database, including 2,036 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 0.16 (2036 hom., cov: 32)
• Consequence: LOC105379034 XR_001742745.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

Genes affected

LOC105379034 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379034	XR_001742745.1	n.1598-1287A>C		intron_variant, non_coding_transcript_variant
LOC105379034	XR_001742746.1	n.340-1287A>C		intron_variant, non_coding_transcript_variant
LOC105379034	XR_007058819.1	n.262-1287A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23974 AN: 151964 Hom.: 2035 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.158 AC: 23976 AN: 152082 Hom.: 2036 Cov.: 32 AF XY: 0.156 AC XY: 11618 AN XY: 74338

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.151

Alfa AF: 0.180 Hom.: 1291

Bravo AF: 0.152

Asia WGS AF: 0.241 AC: 837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6894385; hg19: chr5-73276903;