rs1416733

Variant names:

• chr6-122387909-A-G
• rs1416733

Your query was ambiguous. Multiple possible variants found:

• chr6-122387909-A-G
• chr6-122387909-A-T

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 0.605 in 151,692 control chromosomes in the GnomAD database, including 28,186 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 0.61 (28186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.605 AC: 91751 AN: 151574 Hom.: 28157 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.577

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.605 AC: 91832 AN: 151692 Hom.: 28186 Cov.: 32 AF XY: 0.595 AC XY: 44082 AN XY: 74126

African (AFR) AF: 0.613 AC: 25335 AN: 41356

American (AMR) AF: 0.484 AC: 7380 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2069 AN: 3466

East Asian (EAS) AF: 0.678 AC: 3491 AN: 5152

South Asian (SAS) AF: 0.425 AC: 2050 AN: 4818

European-Finnish (FIN) AF: 0.570 AC: 5980 AN: 10498

Middle Eastern (MID) AF: 0.569 AC: 165 AN: 290

European-Non Finnish (NFE) AF: 0.640 AC: 43452 AN: 67846

Other (OTH) AF: 0.613 AC: 1289 AN: 2104

Alfa AF: 0.619 Hom.: 33805

Bravo AF: 0.607

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.041
DANN	Benign	0.24
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1416733; hg19: chr6-122709054;