20-48591688-T-C

Variant names:

• chr20-48591688-T-C
• rs6090875
• ENST00000775767.1:n.132-16114A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000775767.1(ENSG00000301042):​n.132-16114A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,064 control chromosomes in the GnomAD database, including 3,154 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 0.19 (3154 hom., cov: 32)
• Consequence: ENSG00000301042 ENST00000775767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 2 publications found

Genes affected

ENSG00000301042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775767.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301042	ENST00000775767.1		n.132-16114A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29140 AN: 151946 Hom.: 3155 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.192 AC: 29158 AN: 152064 Hom.: 3154 Cov.: 32 AF XY: 0.190 AC XY: 14152 AN XY: 74342

African (AFR) AF: 0.0980 AC: 4065 AN: 41482

American (AMR) AF: 0.234 AC: 3572 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.0968 AC: 501 AN: 5176

South Asian (SAS) AF: 0.236 AC: 1139 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2122 AN: 10536

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15922 AN: 67980

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.212 Hom.: 1345

Bravo AF: 0.188

Asia WGS AF: 0.144 AC: 499 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.94
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs6090875; hg19: chr20-47208226;