rs7356680

Positions:

• chr5-103854450-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_001742831.2(LOC105379107):​n.277+35216C>T variant causes a intron, non coding transcript 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: LOC105379107 XR_001742831.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

Genes affected

LOC105379107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 75 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379107	XR_001742831.2	n.277+35216C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0157

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.0153

Gnomad4 NFE AF: 0.0421

Gnomad4 OTH AF: 0.0243

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7356680; hg19: chr5-103190151;