rs16119

chr7-24295311-A-G

Variant summary

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

The XR_001745132.2(LOC107986777):n.209+24046T>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 0.506 in 152,066 control chromosomes in the GnomAD database, including 19,880 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 0.51 (19880 hom., cov: 32)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

Genes affected

LOC107986777 (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 = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+24046T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76898 AN: 151948 Hom.: 19870 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.506 AC: 76946 AN: 152066 Hom.: 19880 Cov.: 32 AF XY: 0.510 AC XY: 37936 AN XY: 74330

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.509

Alfa AF: 0.518 Hom.: 4260

Bravo AF: 0.510

Asia WGS AF: 0.568 AC: 1975 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	0.019
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16119; hg19: chr7-24334930;