rs6107848

chr20-6610469-A-Gchr20-6610469-A-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.626 in 152,000 control chromosomes in the GnomAD database, including 30,359 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 0.63 (30359 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.58

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95108 AN: 151882 Hom.: 30324 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.626 AC: 95191 AN: 152000 Hom.: 30359 Cov.: 31 AF XY: 0.630 AC XY: 46831 AN XY: 74288

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.616

Alfa AF: 0.584 Hom.: 4562

Bravo AF: 0.627

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
Cadd	Benign	18
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6107848; hg19: chr20-6591116;