6-130823223-T-C

Variant names:

• chr6-130823223-T-C
• rs1582055

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 0.77 in 152,202 control chromosomes in the GnomAD database, including 45,683 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 0.77 (45683 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.770 AC: 117167 AN: 152084 Hom.: 45636 Cov.: 33

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.770 AC: 117271 AN: 152202 Hom.: 45683 Cov.: 33 AF XY: 0.779 AC XY: 57942 AN XY: 74418

African (AFR) AF: 0.844 AC: 35043 AN: 41534

American (AMR) AF: 0.770 AC: 11776 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5175 AN: 5186

South Asian (SAS) AF: 0.857 AC: 4129 AN: 4820

European-Finnish (FIN) AF: 0.847 AC: 8971 AN: 10590

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.701 AC: 47675 AN: 67996

Other (OTH) AF: 0.717 AC: 1517 AN: 2116

Alfa AF: 0.719 Hom.: 23347

Bravo AF: 0.765

Asia WGS AF: 0.915 AC: 3174 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.2
DANN	Benign	0.89
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1582055; hg19: chr6-131144363;