rs223019

chr7-74161268-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 0.621 in 150,116 control chromosomes in the GnomAD database, including 29,123 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 0.62 (29123 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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: 0.622 AC: 93234 AN: 149998 Hom.: 29101 Cov.: 26

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.621 AC: 93297 AN: 150116 Hom.: 29123 Cov.: 26 AF XY: 0.623 AC XY: 45609 AN XY: 73206

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.631

Alfa AF: 0.619 Hom.: 3231

Bravo AF: 0.621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	0.34
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223019; hg19: chr7-73575598;