rs7356680

Variant names:

• chr5-103854450-C-T
• rs7356680
• ENST00000750993.1:n.191+35216C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000750993.1(ENSG00000297797):​n.191+35216C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 152,174 control chromosomes in the GnomAD database, including 75 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 0.027 (75 hom., cov: 31)
• Consequence: ENSG00000297797 ENST00000750993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 1 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=-1.02).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0274 (4174/152174) while in subpopulation NFE AF = 0.0421 (2862/67996). AF 95% confidence interval is 0.0408. There are 75 homozygotes in GnomAd4. There are 1912 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 75 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379107	XR_001742831.2	n.277+35216C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297797	ENST00000750993.1	n.191+35216C>T		intron_variant	Intron 3 of 4
ENSG00000297797	ENST00000750994.1	n.158-14740C>T		intron_variant	Intron 3 of 4
ENSG00000297797	ENST00000750995.1	n.241-14740C>T		intron_variant	Intron 3 of 3
ENSG00000297797	ENST00000750996.1	n.75+35216C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0275 AC: 4175 AN: 152056 Hom.: 74 Cov.: 31

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0245

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

GnomAD4 genome AF: 0.0274 AC: 4174 AN: 152174 Hom.: 75 Cov.: 31 AF XY: 0.0257 AC XY: 1912 AN XY: 74390

African (AFR) AF: 0.0119 AC: 496 AN: 41534

American (AMR) AF: 0.0157 AC: 240 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3470

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5170

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4826

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10596

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0421 AC: 2862 AN: 67996

Other (OTH) AF: 0.0243 AC: 51 AN: 2102

Alfa AF: 0.0335 Hom.: 12

Bravo AF: 0.0263

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7356680; hg19: chr5-103190151;