rs73366469

Variant names:

• chr7-74619286-T-C
• rs73366469

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 0.116 in 152,182 control chromosomes in the GnomAD database, including 1,191 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 0.12 (1191 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

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 (AFR) allele frequency at 95% confidence interval = 0.166 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: 0.116 AC: 17633 AN: 152064 Hom.: 1183 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0661

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.116 AC: 17677 AN: 152182 Hom.: 1191 Cov.: 31 AF XY: 0.114 AC XY: 8473 AN XY: 74386

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0985

Gnomad4 OTH AF: 0.117

Alfa AF: 0.105 Hom.: 156

Bravo AF: 0.119

Asia WGS AF: 0.111 AC: 388 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	0.49
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73366469; hg19: chr7-74033600;