rs12529935

Positions:

• chr6-90305320-C-T

Variant summary

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

The ENST00000667364.1(ENSG00000260271):​n.30+9784C>T 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 0.0799 in 152,228 control chromosomes in the GnomAD database, including 638 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 0.080 (638 hom., cov: 32)
• Consequence: ENST00000667364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377891	XR_942778.4	n.498+7584C>T		intron_variant, non_coding_transcript_variant
LOC105377891	XR_007059677.1	n.498+7584C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667364.1	n.30+9784C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0799 AC: 12149 AN: 152110 Hom.: 632 Cov.: 32

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.0799 AC: 12166 AN: 152228 Hom.: 638 Cov.: 32 AF XY: 0.0804 AC XY: 5986 AN XY: 74442

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0947 Hom.: 320

Bravo AF: 0.0825

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.49
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12529935; hg19: chr6-91015039;