6-61284899-A-G

Position:

• chr6-61284899-A-G

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 0.835 in 151,678 control chromosomes in the GnomAD database, including 53,114 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 0.84 (53114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 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: 0.835 AC: 126583 AN: 151560 Hom.: 53073 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.835 AC: 126679 AN: 151678 Hom.: 53114 Cov.: 31 AF XY: 0.830 AC XY: 61460 AN XY: 74060

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.820

Alfa AF: 0.867 Hom.: 9069

Bravo AF: 0.830

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1070635; hg19: chr6-61952815;