rs4487548

Variant names:

• chr6-85432693-A-G
• rs4487548

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 0.172 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.260 AC: 10781 AN: 41456

American (AMR) AF: 0.128 AC: 1951 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3472

East Asian (EAS) AF: 0.0622 AC: 322 AN: 5180

South Asian (SAS) AF: 0.168 AC: 811 AN: 4820

European-Finnish (FIN) AF: 0.106 AC: 1119 AN: 10604

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10095 AN: 68002

Other (OTH) AF: 0.159 AC: 335 AN: 2110

Alfa AF: 0.157 Hom.: 1002

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4487548; hg19: chr6-86142411;