rs7548209

Variant names:

• chr1-16122127-G-C
• rs7548209

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 0.358 in 152,094 control chromosomes in the GnomAD database, including 10,399 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 0.36 (10399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 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: 0.358 AC: 54400 AN: 151976 Hom.: 10386 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.358 AC: 54456 AN: 152094 Hom.: 10399 Cov.: 32 AF XY: 0.359 AC XY: 26652 AN XY: 74342

African (AFR) AF: 0.492 AC: 20401 AN: 41476

American (AMR) AF: 0.374 AC: 5718 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3466

East Asian (EAS) AF: 0.150 AC: 776 AN: 5170

South Asian (SAS) AF: 0.362 AC: 1745 AN: 4818

European-Finnish (FIN) AF: 0.279 AC: 2952 AN: 10566

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20443 AN: 67986

Other (OTH) AF: 0.367 AC: 777 AN: 2116

Alfa AF: 0.323 Hom.: 1060

Bravo AF: 0.369

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7548209; hg19: chr1-16448622;