rs284924

Positions:

• chr16-77009729-G-T

Variant summary

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

The XR_007065120.1(LOC124903724):​n.115-1420C>A 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 0.21 in 152,092 control chromosomes in the GnomAD database, including 3,716 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 0.21 (3716 hom., cov: 33)
• Consequence: LOC124903724 XR_007065120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

Genes affected

LOC124903724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903724	XR_007065120.1	n.115-1420C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31920 AN: 151974 Hom.: 3714 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.210 AC: 31914 AN: 152092 Hom.: 3716 Cov.: 33 AF XY: 0.206 AC XY: 15346 AN XY: 74348

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.208

Alfa AF: 0.217 Hom.: 525

Bravo AF: 0.210

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs284924; hg19: chr16-77043626;