rs7549114

Positions:

• chr1-206629756-G-A

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 0.126 in 152,138 control chromosomes in the GnomAD database, including 1,365 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 0.13 (1365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 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: 0.126 AC: 19222 AN: 152020 Hom.: 1365 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0750

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.126 AC: 19222 AN: 152138 Hom.: 1365 Cov.: 32 AF XY: 0.123 AC XY: 9182 AN XY: 74360

Gnomad4 AFR AF: 0.0923

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0755

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.143

Alfa AF: 0.146 Hom.: 3188

Bravo AF: 0.122

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7549114; hg19: chr1-206803101;