rs6433107

Variant names:

• chr2-169122350-T-G
• rs6433107

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 0.758 in 151,940 control chromosomes in the GnomAD database, including 43,973 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 0.76 (43973 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.757 AC: 115002 AN: 151820 Hom.: 43933 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.758 AC: 115095 AN: 151940 Hom.: 43973 Cov.: 31 AF XY: 0.756 AC XY: 56111 AN XY: 74220

African (AFR) AF: 0.803 AC: 33250 AN: 41410

American (AMR) AF: 0.778 AC: 11893 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2157 AN: 5182

South Asian (SAS) AF: 0.773 AC: 3722 AN: 4816

European-Finnish (FIN) AF: 0.747 AC: 7856 AN: 10510

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51318 AN: 67946

Other (OTH) AF: 0.767 AC: 1623 AN: 2116

Alfa AF: 0.761 Hom.: 16879

Bravo AF: 0.758

Asia WGS AF: 0.649 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.66
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6433107; hg19: chr2-169978860;