rs1570311

Variant names:

• chr6-85445433-T-G
• rs1570311

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 0.172 in 152,064 control chromosomes in the GnomAD database, including 2,546 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 0.17 (2546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

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 = 0.257 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: 0.172 AC: 26180 AN: 151944 Hom.: 2546 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.172 AC: 26200 AN: 152064 Hom.: 2546 Cov.: 32 AF XY: 0.168 AC XY: 12494 AN XY: 74334

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0616

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.159

Alfa AF: 0.156 Hom.: 886

Bravo AF: 0.176

Asia WGS AF: 0.114 AC: 397 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	1.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1570311; hg19: chr6-86155151;