rs12549036

Positions:

• chr8-88564845-G-A
• chr8-88564845-G-T

Variant summary

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

The ENST00000665922.1(ENSG00000253553):​n.324+22035G>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 0.127 in 151,156 control chromosomes in the GnomAD database, including 1,804 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 0.13 (1804 hom., cov: 30)
• Consequence: ENST00000665922.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375630	XR_001745653.3	n.355+22035G>A		intron_variant, non_coding_transcript_variant
LOC105375629	XR_928383.4	n.292+1060C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665922.1	n.324+22035G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19219 AN: 151046 Hom.: 1803 Cov.: 30

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.127 AC: 19236 AN: 151156 Hom.: 1804 Cov.: 30 AF XY: 0.132 AC XY: 9763 AN XY: 73856

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.157

Alfa AF: 0.102 Hom.: 145

Bravo AF: 0.146

Asia WGS AF: 0.236 AC: 819 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12549036; hg19: chr8-89577074;