rs810549

Positions:

• chr7-74079203-A-G

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 0.163 in 152,156 control chromosomes in the GnomAD database, including 2,422 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 0.16 (2422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.163 AC: 24783 AN: 152038 Hom.: 2409 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.163 AC: 24813 AN: 152156 Hom.: 2422 Cov.: 32 AF XY: 0.165 AC XY: 12293 AN XY: 74382

Gnomad4 AFR AF: 0.0699

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.218

Alfa AF: 0.191 Hom.: 2259

Bravo AF: 0.167

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
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: rs810549; hg19: chr7-73493533;