rs7690087

Positions:

• chr4-121581655-T-C

Variant summary

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

The XR_939166.2(LOC105377401):​n.182-17T>C variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,972 control chromosomes in the GnomAD database, including 30,421 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 0.62 (30421 hom., cov: 31)
• Consequence: LOC105377401 XR_939166.2 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

Genes affected

LOC105377401 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377401	XR_939166.2	n.182-17T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94323 AN: 151854 Hom.: 30411 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.621 AC: 94375 AN: 151972 Hom.: 30421 Cov.: 31 AF XY: 0.624 AC XY: 46344 AN XY: 74258

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.618

Alfa AF: 0.678 Hom.: 55000

Bravo AF: 0.613

Asia WGS AF: 0.594 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7690087; hg19: chr4-122502810;