rs12961210

Variant names:

• chr18-900522-T-G
• rs12961210
• ENST00000582554.1:n.91-5827A>C

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 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: ENSG00000265671 ENST00000582554.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

Genes affected

ENSG00000265671 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265671	ENST00000582554.1	n.91-5827A>C		intron_variant	Intron 1 of 1	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;