rs7549184

Variant names:

• chr1-215239563-G-A
• rs7549184

Your query was ambiguous. Multiple possible variants found:

• chr1-215239563-G-A
• chr1-215239563-G-C

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 0.712 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.560 AC: 23181 AN: 41372

American (AMR) AF: 0.756 AC: 11525 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3654 AN: 5138

South Asian (SAS) AF: 0.544 AC: 2618 AN: 4812

European-Finnish (FIN) AF: 0.800 AC: 8472 AN: 10588

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53609 AN: 67958

Other (OTH) AF: 0.726 AC: 1534 AN: 2112

Alfa AF: 0.761 Hom.: 170098

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
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs7549184; hg19: chr1-215412906;