6-120873738-G-T

Variant names:

• chr6-120873738-G-T
• rs12527161

Variant summary

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

The variant allele was found at a frequency of 0.33 in 152,060 control chromosomes in the GnomAD database, including 8,864 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 0.33 (8864 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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: 0.330 AC: 50134 AN: 151940 Hom.: 8847 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.330 AC: 50182 AN: 152060 Hom.: 8864 Cov.: 33 AF XY: 0.333 AC XY: 24745 AN XY: 74306

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.337

Alfa AF: 0.258 Hom.: 1824

Bravo AF: 0.347

Asia WGS AF: 0.495 AC: 1720 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	0.87
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12527161; hg19: chr6-121194884;