rs11865624

Variant names:

• chr16-84287168-T-C
• rs11865624
• XM_047435022.1:c.-406+499T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

LOC124903734 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124903734	XM_047435022.1	c.-406+499T>C		intron_variant	Intron 1 of 5		XP_047290978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.319 AC: 13218 AN: 41474

American (AMR) AF: 0.205 AC: 3142 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0740 AC: 257 AN: 3472

East Asian (EAS) AF: 0.187 AC: 967 AN: 5172

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2309 AN: 10574

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0701 AC: 4768 AN: 68022

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.0939 Hom.: 2883

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11865624; hg19: chr16-84320774;