rs4487548

chr6-85432693-A-G

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 0.172 in 152,128 control chromosomes in the GnomAD database, including 2,531 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 0.17 (2531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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: 0.172 AC: 26138 AN: 152010 Hom.: 2532 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0622

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.172 AC: 26157 AN: 152128 Hom.: 2531 Cov.: 32 AF XY: 0.168 AC XY: 12473 AN XY: 74382

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0622

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.159

Alfa AF: 0.156 Hom.: 889

Bravo AF: 0.175

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
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: rs4487548; hg19: chr6-86142411;