rs16930609

chr11-14894362-A-Cchr11-14894362-A-T

Variant summary

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

The XR_007062603.1(LOC124902638):n.1485-4583A>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 0.139 in 152,066 control chromosomes in the GnomAD database, including 1,728 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 0.14 (1728 hom., cov: 32)
• Consequence: LOC124902638 XR_007062603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

LOC124902638 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902638	XR_007062603.1	n.1485-4583A>C		intron_variant, non_coding_transcript_variant
LOC124902638	XR_007062604.1	n.1485-4594A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21134 AN: 151948 Hom.: 1724 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.139 AC: 21172 AN: 152066 Hom.: 1728 Cov.: 32 AF XY: 0.142 AC XY: 10549 AN XY: 74338

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0925

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0529 Hom.: 57

Bravo AF: 0.141

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.1
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16930609; hg19: chr11-14915908;