6-102846145-A-G

Variant names:

• chr6-102846145-A-G
• rs6571064

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 0.0917 in 151,838 control chromosomes in the GnomAD database, including 872 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 0.092 (872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 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: 0.0917 AC: 13914 AN: 151720 Hom.: 872 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.0489

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0917 AC: 13930 AN: 151838 Hom.: 872 Cov.: 32 AF XY: 0.0879 AC XY: 6530 AN XY: 74252

African (AFR) AF: 0.180 AC: 7453 AN: 41490

American (AMR) AF: 0.0649 AC: 988 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0276 AC: 133 AN: 4818

European-Finnish (FIN) AF: 0.0489 AC: 510 AN: 10434

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4349 AN: 67896

Other (OTH) AF: 0.0813 AC: 172 AN: 2116

Alfa AF: 0.0733 Hom.: 353

Bravo AF: 0.0960

Asia WGS AF: 0.0230 AC: 81 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs6571064; hg19: chr6-103294020;