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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379107	XR_001742831.2	n.205-45083T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297797	ENST00000750993.1	n.119-45083T>C		intron_variant	Intron 2 of 4
ENSG00000297797	ENST00000750994.1	n.85-45083T>C		intron_variant	Intron 2 of 4
ENSG00000297797	ENST00000750995.1	n.168-45083T>C		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs320654; hg19: chr5-103109780;