6-61078024-A-G

Variant names:

• chr6-61078024-A-G
• rs3904827

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 0.86 in 152,118 control chromosomes in the GnomAD database, including 56,827 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 0.86 (56827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 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: 0.860 AC: 130763 AN: 152002 Hom.: 56779 Cov.: 32

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.860 AC: 130865 AN: 152118 Hom.: 56827 Cov.: 32 AF XY: 0.852 AC XY: 63331 AN XY: 74308

African (AFR) AF: 0.964 AC: 40096 AN: 41576

American (AMR) AF: 0.856 AC: 13068 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2885 AN: 3470

East Asian (EAS) AF: 0.915 AC: 4735 AN: 5176

South Asian (SAS) AF: 0.734 AC: 3539 AN: 4820

European-Finnish (FIN) AF: 0.701 AC: 7387 AN: 10534

Middle Eastern (MID) AF: 0.890 AC: 260 AN: 292

European-Non Finnish (NFE) AF: 0.828 AC: 56242 AN: 67956

Other (OTH) AF: 0.868 AC: 1832 AN: 2110

Alfa AF: 0.839 Hom.: 6435

Bravo AF: 0.880

Asia WGS AF: 0.831 AC: 2866 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3904827; hg19: chr6-58045771;