rs516636

Variant names:

• chr1-177886382-C-A
• rs516636
• ENST00000664407.1:n.71+33700G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-177886382-C-A
• chr1-177886382-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664407.1(ENSG00000227579):​n.71+33700G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,096 control chromosomes in the GnomAD database, including 2,266 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 0.17 (2266 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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
ENSG00000227579	ENST00000664407.1	n.71+33700G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25266 AN: 151976 Hom.: 2267 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.166 AC: 25273 AN: 152096 Hom.: 2266 Cov.: 32 AF XY: 0.167 AC XY: 12382 AN XY: 74362

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.161

Alfa AF: 0.175 Hom.: 2537

Bravo AF: 0.165

Asia WGS AF: 0.138 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs516636; hg19: chr1-177855517;