rs6449674

Variant names:

• chr5-63700111-T-C
• rs6449674

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;