rs4713897

chr6-35560793-A-Gchr6-35560793-A-T

Variant summary

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

The XR_242006.4(LOC101929309):n.181+15860A>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 0.824 in 151,694 control chromosomes in the GnomAD database, including 51,648 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 0.82 (51648 hom., cov: 29)
• Consequence: LOC101929309 XR_242006.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616

Genes affected

LOC101929309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929309	XR_242006.4	n.181+15860A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.824 AC: 124955 AN: 151576 Hom.: 51592 Cov.: 29

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.824 AC: 125071 AN: 151694 Hom.: 51648 Cov.: 29 AF XY: 0.825 AC XY: 61166 AN XY: 74138

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.801

Alfa AF: 0.816 Hom.: 44437

Bravo AF: 0.827

Asia WGS AF: 0.809 AC: 2811 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	0.24
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713897; hg19: chr6-35528570;