rs12531488

Variant names:

• chr7-145194993-C-T
• rs12531488

Variant summary

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

The variant allele was found at a frequency of 0.248 in 152,068 control chromosomes in the GnomAD database, including 4,820 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 0.25 (4820 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37609 AN: 151950 Hom.: 4814 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.248 AC: 37660 AN: 152068 Hom.: 4820 Cov.: 31 AF XY: 0.246 AC XY: 18319 AN XY: 74334

African (AFR) AF: 0.209 AC: 8678 AN: 41488

American (AMR) AF: 0.310 AC: 4739 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3464

East Asian (EAS) AF: 0.129 AC: 666 AN: 5166

South Asian (SAS) AF: 0.109 AC: 524 AN: 4822

European-Finnish (FIN) AF: 0.263 AC: 2777 AN: 10568

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18370 AN: 67958

Other (OTH) AF: 0.256 AC: 541 AN: 2110

Alfa AF: 0.264 Hom.: 24569

Bravo AF: 0.253

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.20
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12531488; hg19: chr7-144892086;