rs7549184

chr1-215239563-G-Achr1-215239563-G-C

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 0.712 in 151,910 control chromosomes in the GnomAD database, including 39,316 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 0.71 (39316 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.783 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: 0.712 AC: 108055 AN: 151792 Hom.: 39302 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.712 AC: 108111 AN: 151910 Hom.: 39316 Cov.: 31 AF XY: 0.707 AC XY: 52505 AN XY: 74236

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.726

Alfa AF: 0.767 Hom.: 73428

Bravo AF: 0.705

Asia WGS AF: 0.618 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7549184; hg19: chr1-215412906;