rs4896870

chr6-146506145-G-A

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 0.13 in 152,082 control chromosomes in the GnomAD database, including 1,679 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 0.13 (1679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19788 AN: 151964 Hom.: 1680 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.130 AC: 19814 AN: 152082 Hom.: 1679 Cov.: 32 AF XY: 0.126 AC XY: 9403 AN XY: 74340

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.0921

Gnomad4 OTH AF: 0.124

Alfa AF: 0.105 Hom.: 1287

Bravo AF: 0.144

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.9
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896870; hg19: chr6-146827281;