rs5009448

Positions:

• chr6-29972711-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 0.735 in 152,132 control chromosomes in the GnomAD database, including 41,356 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 0.73 (41356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 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: 0.735 AC: 111712 AN: 152014 Hom.: 41315 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.735 AC: 111805 AN: 152132 Hom.: 41356 Cov.: 32 AF XY: 0.734 AC XY: 54619 AN XY: 74368

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.719

Alfa AF: 0.710 Hom.: 19233

Bravo AF: 0.740

Asia WGS AF: 0.724 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5009448; hg19: chr6-29940488;