1-177842882-G-A

Variant names:

• chr1-177842882-G-A
• rs3886720
• ENST00000664407.1:n.71+77200C>T

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.71+77200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,478 control chromosomes in the GnomAD database, including 1,447 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 0.13 (1447 hom., cov: 31)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 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+77200C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20361 AN: 151358 Hom.: 1450 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.134 AC: 20352 AN: 151478 Hom.: 1447 Cov.: 31 AF XY: 0.136 AC XY: 10043 AN XY: 74018

African (AFR) AF: 0.104 AC: 4323 AN: 41376

American (AMR) AF: 0.174 AC: 2640 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 468 AN: 3446

East Asian (EAS) AF: 0.0836 AC: 429 AN: 5134

South Asian (SAS) AF: 0.0857 AC: 411 AN: 4796

European-Finnish (FIN) AF: 0.181 AC: 1893 AN: 10460

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9570 AN: 67760

Other (OTH) AF: 0.168 AC: 352 AN: 2100

Alfa AF: 0.131 Hom.: 161

Bravo AF: 0.134

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.55
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs3886720; hg19: chr1-177812017;