NM_005816.5:c.1180+4422G>T

Variant names:

• chr3-111611214-G-T
• rs16858329
• NM_005816.5:c.1180+4422G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005816.5(CD96):​c.1180+4422G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,978 control chromosomes in the GnomAD database, including 5,878 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 0.26 (5878 hom., cov: 32)
• Consequence: CD96 NM_005816.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 3 publications found

Genes affected

CD96 (HGNC:16892): (CD96 molecule) The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membrane protein. The protein may play a role in the adhesive interactions of activated T and NK cells during the late phase of the immune response. It may also function in antigen presentation. Alternative splicing generates multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2016]

CD96 Gene-Disease associations (from GenCC):

• C syndrome

  Inheritance: Unknown, AD, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005816.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD96	NM_005816.5	MANE Select	c.1180+4422G>T		intron	N/A	NP_005807.1
	CD96	NM_198196.3		c.1228+4422G>T		intron	N/A	NP_937839.1
	CD96	NM_001410800.1		c.1180+4422G>T		intron	N/A	NP_001397729.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD96	ENST00000352690.9	TSL:1 MANE Select	c.1180+4422G>T		intron	N/A	ENSP00000342040.3
	CD96	ENST00000283285.10	TSL:1	c.1228+4422G>T		intron	N/A	ENSP00000283285.5
	CD96	ENST00000494798.2	TSL:2	n.1180+4422G>T		intron	N/A	ENSP00000417152.1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38855 AN: 151860 Hom.: 5862 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.256 AC: 38912 AN: 151978 Hom.: 5878 Cov.: 32 AF XY: 0.257 AC XY: 19107 AN XY: 74282

African (AFR) AF: 0.427 AC: 17668 AN: 41420

American (AMR) AF: 0.201 AC: 3064 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1294 AN: 5172

South Asian (SAS) AF: 0.194 AC: 933 AN: 4810

European-Finnish (FIN) AF: 0.251 AC: 2647 AN: 10544

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12006 AN: 67982

Other (OTH) AF: 0.217 AC: 457 AN: 2110

Alfa AF: 0.214 Hom.: 1672

Bravo AF: 0.261

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.80
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16858329; hg19: chr3-111330061;