rs4429936

Variant names:

• chr6-20526786-T-C
• rs4429936

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 0.483 in 151,980 control chromosomes in the GnomAD database, including 19,347 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 0.48 (19347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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: 0.483 AC: 73324 AN: 151864 Hom.: 19361 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.483 AC: 73334 AN: 151980 Hom.: 19347 Cov.: 32 AF XY: 0.488 AC XY: 36243 AN XY: 74268

African (AFR) AF: 0.258 AC: 10680 AN: 41470

American (AMR) AF: 0.543 AC: 8282 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2071 AN: 3472

East Asian (EAS) AF: 0.781 AC: 4039 AN: 5170

South Asian (SAS) AF: 0.598 AC: 2877 AN: 4814

European-Finnish (FIN) AF: 0.555 AC: 5843 AN: 10534

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37719 AN: 67964

Other (OTH) AF: 0.518 AC: 1092 AN: 2110

Alfa AF: 0.539 Hom.: 100411

Bravo AF: 0.473

Asia WGS AF: 0.611 AC: 2125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4429936; hg19: chr6-20527017;