rs4722551

chr7-25952206-T-Cchr7-25952206-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_927114.3(LOC105375199):n.1314-12745A>G 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 0.131 in 152,144 control chromosomes in the GnomAD database, including 1,655 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 0.13 (1655 hom., cov: 32)
• Consequence: LOC105375199 XR_927114.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

LOC105375199 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375199	XR_927114.3	n.1314-12745A>G		intron_variant, non_coding_transcript_variant
LOC105375199	XR_927122.3	n.541-12745A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19863 AN: 152026 Hom.: 1651 Cov.: 32

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.131 AC: 19881 AN: 152144 Hom.: 1655 Cov.: 32 AF XY: 0.133 AC XY: 9917 AN XY: 74364

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0233

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.119

Alfa AF: 0.149 Hom.: 3182

Bravo AF: 0.120

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	12
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4722551; hg19: chr7-25991826;