rs6127921

Variant names:

• chr20-57063694-A-C
• rs6127921
• ENST00000748753.1:n.185+166T>G

Variant summary

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

The ENST00000748753.1(ENSG00000297537):​n.185+166T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,096 control chromosomes in the GnomAD database, including 2,370 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 0.16 (2370 hom., cov: 32)
• Consequence: ENSG00000297537 ENST00000748753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841
• Publications: 20 publications found

Genes affected

ENSG00000297537 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.412 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
ENSG00000297537	ENST00000748753.1	n.185+166T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24440 AN: 151976 Hom.: 2373 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.161 AC: 24438 AN: 152096 Hom.: 2370 Cov.: 32 AF XY: 0.160 AC XY: 11930 AN XY: 74350

African (AFR) AF: 0.162 AC: 6742 AN: 41492

American (AMR) AF: 0.276 AC: 4218 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 626 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2204 AN: 5158

South Asian (SAS) AF: 0.114 AC: 549 AN: 4806

European-Finnish (FIN) AF: 0.0616 AC: 653 AN: 10608

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8850 AN: 67986

Other (OTH) AF: 0.175 AC: 369 AN: 2108

Alfa AF: 0.150 Hom.: 6002

Bravo AF: 0.183

Asia WGS AF: 0.281 AC: 976 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	5.1
DANN	Benign	0.65
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs6127921; hg19: chr20-55638750;