4-6269316-A-T

Variant names:

• chr4-6269316-A-T
• rs4320200

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 0.569 in 152,118 control chromosomes in the GnomAD database, including 25,534 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 0.57 (25534 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86456 AN: 152000 Hom.: 25512 Cov.: 34

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.569 AC: 86519 AN: 152118 Hom.: 25534 Cov.: 34 AF XY: 0.574 AC XY: 42656 AN XY: 74344

African (AFR) AF: 0.463 AC: 19187 AN: 41478

American (AMR) AF: 0.655 AC: 10020 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2308 AN: 3470

East Asian (EAS) AF: 0.935 AC: 4850 AN: 5186

South Asian (SAS) AF: 0.667 AC: 3216 AN: 4820

European-Finnish (FIN) AF: 0.547 AC: 5785 AN: 10574

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39303 AN: 67988

Other (OTH) AF: 0.596 AC: 1259 AN: 2114

Alfa AF: 0.572 Hom.: 3116

Bravo AF: 0.573

Asia WGS AF: 0.769 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.5
DANN	Benign	0.85
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4320200; hg19: chr4-6271043;