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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.591 AC: 24488 AN: 41404

American (AMR) AF: 0.673 AC: 10263 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2544 AN: 3464

East Asian (EAS) AF: 0.715 AC: 3680 AN: 5148

South Asian (SAS) AF: 0.774 AC: 3716 AN: 4804

European-Finnish (FIN) AF: 0.843 AC: 8927 AN: 10584

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.750 AC: 50983 AN: 67952

Other (OTH) AF: 0.694 AC: 1465 AN: 2112

Alfa AF: 0.729 Hom.: 183213

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1923380; hg19: chr6-165491551;