rs1548513

Variant names:

• chr6-30419910-A-G
• rs1548513

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 0.163 in 151,808 control chromosomes in the GnomAD database, including 2,210 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 0.16 (2210 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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: 0.163 AC: 24753 AN: 151690 Hom.: 2209 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.163 AC: 24767 AN: 151808 Hom.: 2210 Cov.: 31 AF XY: 0.158 AC XY: 11754 AN XY: 74198

African (AFR) AF: 0.239 AC: 9896 AN: 41344

American (AMR) AF: 0.106 AC: 1616 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.0316 AC: 163 AN: 5158

South Asian (SAS) AF: 0.140 AC: 677 AN: 4820

European-Finnish (FIN) AF: 0.0894 AC: 940 AN: 10518

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10530 AN: 67956

Other (OTH) AF: 0.152 AC: 320 AN: 2106

Alfa AF: 0.154 Hom.: 3744

Bravo AF: 0.171

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	8.6
DANN	Benign	0.92
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1548513; hg19: chr6-30387687;