chr17-6124864-A-G

Variant names:

• chr17-6124864-A-G
• rs8069938

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 0.258 in 152,028 control chromosomes in the GnomAD database, including 5,658 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 0.26 (5658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 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: 0.258 AC: 39265 AN: 151910 Hom.: 5654 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.258 AC: 39271 AN: 152028 Hom.: 5658 Cov.: 32 AF XY: 0.259 AC XY: 19222 AN XY: 74338

African (AFR) AF: 0.121 AC: 5009 AN: 41456

American (AMR) AF: 0.293 AC: 4478 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1904 AN: 5166

South Asian (SAS) AF: 0.208 AC: 1006 AN: 4830

European-Finnish (FIN) AF: 0.324 AC: 3422 AN: 10548

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21873 AN: 67968

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.298 Hom.: 10630

Bravo AF: 0.252

Asia WGS AF: 0.230 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.72
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs8069938; hg19: chr17-6028184;