4-27058367-A-T

Variant names:

• chr4-27058367-A-T
• rs6829685

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.050 (385 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.0500 AC: 5284 AN: 105780 Hom.: 385 Cov.: 19

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000765

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00595

Gnomad NFE AF: 0.000431

Gnomad OTH AF: 0.0336

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

GnomAD4 genome AF: 0.0501 AC: 5299 AN: 105844 Hom.: 385 Cov.: 19 AF XY: 0.0509 AC XY: 2519 AN XY: 49478

African (AFR) AF: 0.179 AC: 5020 AN: 28072

American (AMR) AF: 0.0237 AC: 204 AN: 8602

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2844

East Asian (EAS) AF: 0.00 AC: 0 AN: 2910

South Asian (SAS) AF: 0.000765 AC: 2 AN: 2614

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5004

Middle Eastern (MID) AF: 0.00633 AC: 1 AN: 158

European-Non Finnish (NFE) AF: 0.000431 AC: 23 AN: 53384

Other (OTH) AF: 0.0334 AC: 49 AN: 1468

Alfa AF: 0.0345 Hom.: 38

Bravo AF: 0.0493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.80
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs6829685; hg19: chr4-27059989;