rs320654

Variant names:

• chr5-103774079-T-C
• rs320654
• ENST00000750993.1:n.119-45083T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-103774079-T-C
• chr5-103774079-T-G

Variant summary

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

The ENST00000750993.1(ENSG00000297797):​n.119-45083T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,034 control chromosomes in the GnomAD database, including 9,177 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 0.34 (9177 hom., cov: 33)
• Consequence: ENSG00000297797 ENST00000750993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

Genes affected

ENSG00000297797 (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 = 0.4 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750993.1. 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
	ENSG00000297797	ENST00000750993.1		n.119-45083T>C		intron	N/A
	ENSG00000297797	ENST00000750994.1		n.85-45083T>C		intron	N/A
	ENSG00000297797	ENST00000750995.1		n.168-45083T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51392 AN: 151916 Hom.: 9170 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.338 AC: 51408 AN: 152034 Hom.: 9177 Cov.: 33 AF XY: 0.335 AC XY: 24910 AN XY: 74326

African (AFR) AF: 0.245 AC: 10161 AN: 41508

American (AMR) AF: 0.311 AC: 4751 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3466

East Asian (EAS) AF: 0.223 AC: 1155 AN: 5180

South Asian (SAS) AF: 0.353 AC: 1702 AN: 4818

European-Finnish (FIN) AF: 0.330 AC: 3491 AN: 10564

Middle Eastern (MID) AF: 0.455 AC: 132 AN: 290

European-Non Finnish (NFE) AF: 0.404 AC: 27415 AN: 67940

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.382 Hom.: 47761

Bravo AF: 0.332

Asia WGS AF: 0.252 AC: 880 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	0.026
DANN	Benign	0.61
PhyloP100		-1.2

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: rs320654;

hg19: chr5-103109780;