rs7549830

Variant names:

• chr1-161718641-T-C
• rs7549830

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 0.185 in 152,206 control chromosomes in the GnomAD database, including 3,289 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 0.18 (3289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.184 AC: 28045 AN: 152088 Hom.: 3281 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.185 AC: 28085 AN: 152206 Hom.: 3289 Cov.: 33 AF XY: 0.184 AC XY: 13703 AN XY: 74404

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.149

Alfa AF: 0.142 Hom.: 810

Bravo AF: 0.185

Asia WGS AF: 0.286 AC: 995 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	1.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7549830; hg19: chr1-161688431;