rs73366469

Positions:

• chr7-74619286-T-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 0.116 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;