rs1674067

chr6-6339144-A-Gchr6-6339144-A-T

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 0.841 in 152,204 control chromosomes in the GnomAD database, including 54,209 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 0.84 (54209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 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: 0.842 AC: 127990 AN: 152086 Hom.: 54176 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.841 AC: 128077 AN: 152204 Hom.: 54209 Cov.: 32 AF XY: 0.835 AC XY: 62155 AN XY: 74414

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.819

Alfa AF: 0.867 Hom.: 30854

Bravo AF: 0.839

Asia WGS AF: 0.663 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	11
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1674067; hg19: chr6-6339377;