5-103617536-C-T

Variant names:

• chr5-103617536-C-T
• rs7704545
• ENST00000750993.1:n.63+10156C>T

Variant summary

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

The ENST00000750993.1(ENSG00000297797):​n.63+10156C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,950 control chromosomes in the GnomAD database, including 10,464 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 0.36 (10464 hom., cov: 32)
• Consequence: ENSG00000297797 ENST00000750993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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.63+10156C>T		intron	N/A
	ENSG00000297797	ENST00000750994.1		n.29+10156C>T		intron	N/A
	ENSG00000297797	ENST00000750995.1		n.112+10156C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55039 AN: 151832 Hom.: 10461 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.362 AC: 55076 AN: 151950 Hom.: 10464 Cov.: 32 AF XY: 0.369 AC XY: 27437 AN XY: 74266

African (AFR) AF: 0.336 AC: 13958 AN: 41482

American (AMR) AF: 0.400 AC: 6104 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.736 AC: 3800 AN: 5162

South Asian (SAS) AF: 0.587 AC: 2823 AN: 4812

European-Finnish (FIN) AF: 0.352 AC: 3715 AN: 10562

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22286 AN: 67888

Other (OTH) AF: 0.373 AC: 786 AN: 2108

Alfa AF: 0.347 Hom.: 1691

Bravo AF: 0.361

Asia WGS AF: 0.625 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs7704545; hg19: chr5-102953237;