rs16948719

Positions:

• chr15-65413633-C-T

Variant summary

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

The NM_020962.3(IGDCC4):​c.71-2263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,194 control chromosomes in the GnomAD database, including 4,158 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 (4158 hom., cov: 32)
• Consequence: IGDCC4 NM_020962.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

IGDCC4 (HGNC:13770): (immunoglobulin superfamily DCC subclass member 4) Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGDCC4	NM_020962.3	c.71-2263G>A		intron_variant		ENST00000352385.3	NP_066013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGDCC4	ENST00000352385.3	c.71-2263G>A		intron_variant		1	NM_020962.3	ENSP00000319623.3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31504 AN: 152076 Hom.: 4154 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.207 AC: 31516 AN: 152194 Hom.: 4158 Cov.: 32 AF XY: 0.215 AC XY: 16011 AN XY: 74400

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.206

Alfa AF: 0.209 Hom.: 442

Bravo AF: 0.196

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs16948719; hg19: chr15-65705971;