rs4896870

Variant names:

• chr6-146506145-G-A
• rs4896870

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 0.13 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.226 AC: 9370 AN: 41484

American (AMR) AF: 0.156 AC: 2374 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3464

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5172

South Asian (SAS) AF: 0.131 AC: 631 AN: 4826

European-Finnish (FIN) AF: 0.0363 AC: 385 AN: 10614

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0921 AC: 6262 AN: 67966

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.110 Hom.: 1957

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
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs4896870; hg19: chr6-146827281;