rs575076

Variant names:

• chr6-145286310-T-G
• rs575076

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 0.138 in 151,532 control chromosomes in the GnomAD database, including 1,652 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 0.14 (1652 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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: 0.138 AC: 20961 AN: 151412 Hom.: 1649 Cov.: 30

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.000585

Gnomad SAS AF: 0.0144

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.138 AC: 20980 AN: 151532 Hom.: 1652 Cov.: 30 AF XY: 0.136 AC XY: 10038 AN XY: 74022

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.0973

Gnomad4 ASJ AF: 0.0998

Gnomad4 EAS AF: 0.000587

Gnomad4 SAS AF: 0.0140

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.141

Alfa AF: 0.137 Hom.: 182

Bravo AF: 0.140

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.57
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs575076; hg19: chr6-145607446;