rs11865624

Positions:

• chr16-84287168-T-C

Variant summary

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

The XM_047435022.1(LOC124903734):​c.-406+499T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,154 control chromosomes in the GnomAD database, including 3,199 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 0.17 (3199 hom., cov: 32)
• Consequence: LOC124903734 XM_047435022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

LOC124903734 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903734	XM_047435022.1	c.-406+499T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25995 AN: 152036 Hom.: 3188 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0740

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0701

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.171 AC: 26049 AN: 152154 Hom.: 3199 Cov.: 32 AF XY: 0.178 AC XY: 13254 AN XY: 74394

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.0740

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.0701

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0866 Hom.: 1620

Bravo AF: 0.177

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11865624; hg19: chr16-84320774;