rs6077130

Variant names:

• chr20-7011641-T-C
• rs6077130

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0444 in 152,250 control chromosomes in the GnomAD database, including 174 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 0.044 (174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0444 (6759/152250) while in subpopulation NFE AF = 0.0464 (3155/68010). AF 95% confidence interval is 0.045. There are 174 homozygotes in GnomAd4. There are 3429 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 174 gene

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: 0.0444 AC: 6749 AN: 152132 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0444 AC: 6759 AN: 152250 Hom.: 174 Cov.: 32 AF XY: 0.0461 AC XY: 3429 AN XY: 74430

African (AFR) AF: 0.0436 AC: 1813 AN: 41552

American (AMR) AF: 0.0354 AC: 542 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4820

European-Finnish (FIN) AF: 0.0918 AC: 973 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0464 AC: 3155 AN: 68010

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0445 Hom.: 29

Bravo AF: 0.0395

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs6077130; hg19: chr20-6992288;