rs174760

Variant names:

• chr22-29304546-C-G
• rs174760
• ENST00000780180.1:n.118-4711G>C

Variant summary

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

The ENST00000780180.1(ENSG00000301612):​n.118-4711G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,026 control chromosomes in the GnomAD database, including 2,239 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 0.16 (2239 hom., cov: 31)
• Consequence: ENSG00000301612 ENST00000780180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 3 publications found

Genes affected

ENSG00000301612 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780180.1. 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
	ENSG00000301612	ENST00000780180.1		n.118-4711G>C		intron	N/A
	ENSG00000301612	ENST00000780181.1		n.226+1920G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24653 AN: 151906 Hom.: 2239 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.162 AC: 24655 AN: 152026 Hom.: 2239 Cov.: 31 AF XY: 0.158 AC XY: 11773 AN XY: 74312

African (AFR) AF: 0.112 AC: 4658 AN: 41448

American (AMR) AF: 0.149 AC: 2280 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3468

East Asian (EAS) AF: 0.0418 AC: 216 AN: 5172

South Asian (SAS) AF: 0.0998 AC: 481 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10578

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14000 AN: 67956

Other (OTH) AF: 0.173 AC: 365 AN: 2112

Alfa AF: 0.179 Hom.: 334

Bravo AF: 0.161

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.63
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs174760;

hg19: chr22-29700536;