rs6449674

Positions:

• chr5-63700111-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 0.476 in 152,042 control chromosomes in the GnomAD database, including 18,306 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 0.48 (18306 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 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: 0.476 AC: 72324 AN: 151922 Hom.: 18288 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.476 AC: 72376 AN: 152042 Hom.: 18306 Cov.: 33 AF XY: 0.486 AC XY: 36148 AN XY: 74316

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.491

Alfa AF: 0.484 Hom.: 3093

Bravo AF: 0.463

Asia WGS AF: 0.734 AC: 2546 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449674; hg19: chr5-62995938;