rs6885006

chr5-101693040-T-G

Variant summary

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

The XR_007058891.1(LOC105379102):n.388+37169A>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 0.0568 in 152,138 control chromosomes in the GnomAD database, including 270 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 0.057 (270 hom., cov: 32)
• Consequence: LOC105379102 XR_007058891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

Genes affected

LOC105379102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379102	XR_007058891.1	n.388+37169A>C		intron_variant, non_coding_transcript_variant
LOC105379102	XR_948628.3	n.388+37169A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0569 AC: 8643 AN: 152020 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0406

Gnomad ASJ AF: 0.0641

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0644

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0568 AC: 8644 AN: 152138 Hom.: 270 Cov.: 32 AF XY: 0.0555 AC XY: 4125 AN XY: 74366

Gnomad4 AFR AF: 0.0519

Gnomad4 AMR AF: 0.0405

Gnomad4 ASJ AF: 0.0641

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0334

Gnomad4 FIN AF: 0.0644

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.0526

Alfa AF: 0.0626 Hom.: 476

Bravo AF: 0.0548

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2
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: rs6885006; hg19: chr5-101028744;