rs6449004

Variant names:

• chr4-14163091-T-A
• rs6449004

Your query was ambiguous. Multiple possible variants found:

• chr4-14163091-T-A
• chr4-14163091-T-C
• chr4-14163091-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 0.678 in 151,860 control chromosomes in the GnomAD database, including 35,558 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 0.68 (35558 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.678 AC: 102806 AN: 151742 Hom.: 35501 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.678 AC: 102921 AN: 151860 Hom.: 35558 Cov.: 31 AF XY: 0.682 AC XY: 50657 AN XY: 74230

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.678

Alfa AF: 0.648 Hom.: 4026

Bravo AF: 0.688

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449004; hg19: chr4-14164715;