rs17753780

Positions:

• chr7-4462654-C-A
• chr7-4462654-C-G
• chr7-4462654-C-T

Variant summary

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

The XR_007060198.1(LOC124901579):​n.46-13506C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 149,442 control chromosomes in the GnomAD database, including 39,388 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 0.72 (39388 hom., cov: 27)
• Consequence: LOC124901579 XR_007060198.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

LOC124901579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901579	XR_007060198.1	n.46-13506C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.720 AC: 107500 AN: 149384 Hom.: 39372 Cov.: 27

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.720 AC: 107543 AN: 149442 Hom.: 39388 Cov.: 27 AF XY: 0.722 AC XY: 52434 AN XY: 72626

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.692

Alfa AF: 0.662 Hom.: 59518

Bravo AF: 0.718

Asia WGS AF: 0.715 AC: 2486 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17753780; hg19: chr7-4502285;