rs1923380

Variant names:

• chr6-165078062-G-A
• rs1923380

Your query was ambiguous. Multiple possible variants found:

• chr6-165078062-G-A
• chr6-165078062-G-C
• chr6-165078062-G-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 0.704 in 151,922 control chromosomes in the GnomAD database, including 38,229 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 0.70 (38229 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

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 (SAS) allele frequency at 95% confidence interval = 0.753 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: 0.704 AC: 106888 AN: 151804 Hom.: 38224 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.704 AC: 106935 AN: 151922 Hom.: 38229 Cov.: 31 AF XY: 0.709 AC XY: 52648 AN XY: 74236

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.694

Alfa AF: 0.734 Hom.: 87210

Bravo AF: 0.684

Asia WGS AF: 0.686 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923380; hg19: chr6-165491551;