4-28663346-T-C

Variant names:

• chr4-28663346-T-C
• rs6815271

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.9 in 152,242 control chromosomes in the GnomAD database, including 61,889 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 0.90 (61889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.900 AC: 136929 AN: 152124 Hom.: 61831 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.900 AC: 137047 AN: 152242 Hom.: 61889 Cov.: 32 AF XY: 0.904 AC XY: 67264 AN XY: 74434

Gnomad4 AFR AF: 0.972

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.888

Alfa AF: 0.863 Hom.: 22358

Bravo AF: 0.899

Asia WGS AF: 0.958 AC: 3332 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	0.14
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6815271; hg19: chr4-28664968;