rs17753780

Variant names:

• chr7-4462654-C-A
• rs17753780
• ENST00000741164.1:n.175-25343C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-4462654-C-A
• chr7-4462654-C-G
• chr7-4462654-C-T

Variant summary

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

The ENST00000741164.1(ENSG00000296681):​n.175-25343C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 149,442 control chromosomes in the GnomAD database, including 39,388 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 0.72 (39388 hom., cov: 27)
• Consequence: ENSG00000296681 ENST00000741164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 4 publications found

Genes affected

ENSG00000296681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741164.1. 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
	ENSG00000296681	ENST00000741164.1		n.175-25343C>A		intron	N/A
	ENSG00000296681	ENST00000741167.1		n.215-25343C>A		intron	N/A
	ENSG00000296681	ENST00000741168.1		n.255-13506C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.720 AC: 107500 AN: 149384 Hom.: 39372 Cov.: 27

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.720 AC: 107543 AN: 149442 Hom.: 39388 Cov.: 27 AF XY: 0.722 AC XY: 52434 AN XY: 72626

African (AFR) AF: 0.869 AC: 35283 AN: 40606

American (AMR) AF: 0.641 AC: 9643 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2213 AN: 3452

East Asian (EAS) AF: 0.769 AC: 3935 AN: 5114

South Asian (SAS) AF: 0.674 AC: 3204 AN: 4752

European-Finnish (FIN) AF: 0.725 AC: 6883 AN: 9500

Middle Eastern (MID) AF: 0.686 AC: 192 AN: 280

European-Non Finnish (NFE) AF: 0.653 AC: 44238 AN: 67720

Other (OTH) AF: 0.692 AC: 1429 AN: 2064

Alfa AF: 0.671 Hom.: 143544

Bravo AF: 0.718

Asia WGS AF: 0.715 AC: 2486 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.70
PhyloP100		-0.0080

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: rs17753780;

hg19: chr7-4502285;