rs12207515

Positions:

• chr6-90891816-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001744259.1(LOC107986623):​n.1244-16240G>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 0.0923 in 151,202 control chromosomes in the GnomAD database, including 677 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 0.092 (677 hom., cov: 31)
• Consequence: LOC107986623 XR_001744259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

LOC107986623 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1244-16240G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 13947 AN: 151088 Hom.: 677 Cov.: 31

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.0932

Gnomad EAS AF: 0.00797

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0923 AC: 13958 AN: 151202 Hom.: 677 Cov.: 31 AF XY: 0.0911 AC XY: 6723 AN XY: 73824

Gnomad4 AFR AF: 0.0855

Gnomad4 AMR AF: 0.0696

Gnomad4 ASJ AF: 0.0932

Gnomad4 EAS AF: 0.00779

Gnomad4 SAS AF: 0.0881

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.105 Hom.: 500

Bravo AF: 0.0874

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	20
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12207515; hg19: chr6-91601534;