rs11969893

Positions:

• chr6-100947531-G-A
• chr6-100947531-G-T

Variant summary

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

The XR_007059692.1(LOC107984041):​n.247-15155G>A 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 0.0376 in 152,112 control chromosomes in the GnomAD database, including 138 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 0.038 (138 hom., cov: 31)
• Consequence: LOC107984041 XR_007059692.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

Genes affected

LOC107984041 (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 (AFR) allele frequency at 95% confidence interval = 0.0549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984041	XR_007059692.1	n.247-15155G>A		intron_variant, non_coding_transcript_variant
LOC107984041	XR_002956381.2	n.247-15155G>A		intron_variant, non_coding_transcript_variant
LOC107984041	XR_002956382.2	n.247-15155G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 5711 AN: 151994 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0376 AC: 5717 AN: 152112 Hom.: 138 Cov.: 31 AF XY: 0.0369 AC XY: 2746 AN XY: 74364

Gnomad4 AFR AF: 0.0569

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.000969

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.0483

Gnomad4 NFE AF: 0.0324

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0285 Hom.: 68

Bravo AF: 0.0368

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11969893; hg19: chr6-101395407;