1-177599664-C-G

Variant names:

• chr1-177599664-C-G
• rs16851585
• ENST00000438575.7:n.92-22714G>C

Variant summary

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

The ENST00000438575.7(ENSG00000227579):​n.92-22714G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,124 control chromosomes in the GnomAD database, including 1,663 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 0.14 (1663 hom., cov: 33)
• Consequence: ENSG00000227579 ENST00000438575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 3 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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438575.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227579	ENST00000438575.7	TSL:3	n.92-22714G>C		intron	N/A
	ENSG00000227579	ENST00000663166.1		n.277-22714G>C		intron	N/A
	ENSG00000227579	ENST00000663978.1		n.180-22714G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20571 AN: 152004 Hom.: 1667 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.135 AC: 20574 AN: 152124 Hom.: 1663 Cov.: 33 AF XY: 0.141 AC XY: 10491 AN XY: 74362

African (AFR) AF: 0.150 AC: 6216 AN: 41486

American (AMR) AF: 0.127 AC: 1940 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2111 AN: 5158

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1380 AN: 10558

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6958 AN: 68024

Other (OTH) AF: 0.130 AC: 276 AN: 2116

Alfa AF: 0.126 Hom.: 163

Bravo AF: 0.134

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.8
DANN	Benign	0.73
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs16851585; hg19: chr1-177568799;