rs12529935

Variant names:

• chr6-90305320-C-T
• rs12529935
• ENST00000654016.1:n.43+8311C>T

Variant summary

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

The ENST00000654016.1(ENSG00000260271):​n.43+8311C>T variant causes a intron 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: ENSG00000260271 ENST00000654016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 12 publications found

Genes affected

ENSG00000260271 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105377891	XR_007059677.1	n.498+7584C>T		intron_variant	Intron 1 of 4
LOC105377891	XR_942778.4	n.498+7584C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260271	ENST00000654016.1	n.43+8311C>T		intron_variant	Intron 1 of 7
ENSG00000260271	ENST00000663503.1	n.85+8311C>T		intron_variant	Intron 1 of 4
ENSG00000260271	ENST00000667364.1	n.30+9784C>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.0280 AC: 1162 AN: 41532

American (AMR) AF: 0.125 AC: 1919 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3470

East Asian (EAS) AF: 0.0907 AC: 470 AN: 5182

South Asian (SAS) AF: 0.125 AC: 602 AN: 4814

European-Finnish (FIN) AF: 0.0559 AC: 593 AN: 10612

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6515 AN: 68002

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.0852 Hom.: 452

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12529935; hg19: chr6-91015039;