rs6885006

Variant names:

• chr5-101693040-T-G
• rs6885006
• XR_007058891.1:n.388+37169A>C

Variant summary

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

The XR_007058891.1(LOC105379102):​n.388+37169A>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 1 publications found

Genes affected

LOC105379102 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105379102	XR_007058891.1	n.388+37169A>C		intron_variant	Intron 3 of 5
LOC105379102	XR_948628.3	n.388+37169A>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0519 AC: 2154 AN: 41538

American (AMR) AF: 0.0405 AC: 618 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0641 AC: 222 AN: 3466

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0334 AC: 161 AN: 4826

European-Finnish (FIN) AF: 0.0644 AC: 682 AN: 10590

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0674 AC: 4584 AN: 67972

Other (OTH) AF: 0.0526 AC: 111 AN: 2112

Alfa AF: 0.0625 Hom.: 589

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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6885006; hg19: chr5-101028744;