rs633715

Variant names:

• chr1-177883445-T-C
• rs633715
• ENST00000664407.1:n.71+36637A>G

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.71+36637A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,998 control chromosomes in the GnomAD database, including 2,308 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 (2308 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 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+36637A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25311 AN: 151880 Hom.: 2309 Cov.: 32

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.167 AC: 25320 AN: 151998 Hom.: 2308 Cov.: 32 AF XY: 0.168 AC XY: 12509 AN XY: 74288

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.159

Alfa AF: 0.185 Hom.: 4744

Bravo AF: 0.163

Asia WGS AF: 0.139 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs633715; hg19: chr1-177852580;