rs633715

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 52 publications found

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664407.1. 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
	ENSG00000227579	ENST00000664407.1		n.71+36637A>G		intron	N/A

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

African (AFR) AF: 0.0983 AC: 4076 AN: 41458

American (AMR) AF: 0.195 AC: 2976 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3460

East Asian (EAS) AF: 0.175 AC: 901 AN: 5160

South Asian (SAS) AF: 0.147 AC: 708 AN: 4812

European-Finnish (FIN) AF: 0.218 AC: 2298 AN: 10564

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13446 AN: 67950

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.185 Hom.: 9525

Bravo AF: 0.163

Asia WGS AF: 0.139 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.40
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs633715; hg19: chr1-177852580;