rs1674067

Variant names:

• chr6-6339144-A-G
• rs1674067

Your query was ambiguous. Multiple possible variants found:

• chr6-6339144-A-G
• chr6-6339144-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.837 AC: 34736 AN: 41504

American (AMR) AF: 0.778 AC: 11896 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2709 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3268 AN: 5182

South Asian (SAS) AF: 0.670 AC: 3229 AN: 4816

European-Finnish (FIN) AF: 0.854 AC: 9031 AN: 10580

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60470 AN: 68038

Other (OTH) AF: 0.819 AC: 1730 AN: 2112

Alfa AF: 0.869 Hom.: 40902

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
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs1674067; hg19: chr6-6339377;