rs12961210

Positions:

• chr18-900522-T-G

Variant summary

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

The ENST00000582554.1(ENSG00000265671):​n.91-5827A>C 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 0.288 in 152,088 control chromosomes in the GnomAD database, including 6,485 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 0.29 (6485 hom., cov: 32)
• Consequence: ENST00000582554.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000582554.1	n.91-5827A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43879 AN: 151970 Hom.: 6492 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.288 AC: 43865 AN: 152088 Hom.: 6485 Cov.: 32 AF XY: 0.285 AC XY: 21207 AN XY: 74358

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.293

Alfa AF: 0.312 Hom.: 12123

Bravo AF: 0.294

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12961210; hg19: chr18-900523;