rs84034

Positions:

• chr7-153330567-T-C
• chr7-153330567-T-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 0.7 in 152,140 control chromosomes in the GnomAD database, including 37,408 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 0.70 (37408 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.879

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 (AMR) allele frequency at 95% confidence interval = 0.724 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: 0.700 AC: 106447 AN: 152022 Hom.: 37377 Cov.: 33

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.700 AC: 106529 AN: 152140 Hom.: 37408 Cov.: 33 AF XY: 0.701 AC XY: 52126 AN XY: 74362

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.712

Alfa AF: 0.713 Hom.: 37825

Bravo AF: 0.700

Asia WGS AF: 0.662 AC: 2301 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	7.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs84034; hg19: chr7-153027652;