rs4719841

chr7-25957916-A-Gchr7-25957916-A-T

Variant summary

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

The XR_927114.3(LOC105375199):n.1314-18455T>C 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 0.378 in 151,984 control chromosomes in the GnomAD database, including 11,435 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 0.38 (11435 hom., cov: 31)
• Consequence: LOC105375199 XR_927114.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.790

Genes affected

LOC105375199 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375199	XR_927114.3	n.1314-18455T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57452 AN: 151864 Hom.: 11441 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.378 AC: 57459 AN: 151984 Hom.: 11435 Cov.: 31 AF XY: 0.379 AC XY: 28166 AN XY: 74298

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.423

Alfa AF: 0.424 Hom.: 29497

Bravo AF: 0.375

Asia WGS AF: 0.556 AC: 1932 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	13
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: rs4719841; hg19: chr7-25997536;