NM_152406.4:c.16+9150T>C

Variant names:

• chr5-149281134-T-C
• rs10062080
• NM_152406.4:c.16+9150T>C

Variant summary

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

The NM_152406.4(AFAP1L1):​c.16+9150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,006 control chromosomes in the GnomAD database, including 18,345 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 0.48 (18345 hom., cov: 32)
• Consequence: AFAP1L1 NM_152406.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

AFAP1L1 (HGNC:26714): (actin filament associated protein 1 like 1) Predicted to enable SH3 domain binding activity. Predicted to be located in cell junction; cell projection; and podosome. Predicted to be active in cytosol. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AFAP1L1	NM_152406.4	c.16+9150T>C		intron_variant	Intron 1 of 18	ENST00000296721.9	NP_689619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AFAP1L1	ENST00000296721.9	c.16+9150T>C		intron_variant	Intron 1 of 18	1	NM_152406.4	ENSP00000296721.4
AFAP1L1	ENST00000515000.1	c.16+9150T>C		intron_variant	Intron 1 of 17	1		ENSP00000424427.1
AFAP1L1	ENST00000455574.6	n.114+9150T>C		intron_variant	Intron 1 of 8	1
AFAP1L1	ENST00000522492.1	n.90+9150T>C		intron_variant	Intron 1 of 7	3

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73362 AN: 151888 Hom.: 18307 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.483 AC: 73440 AN: 152006 Hom.: 18345 Cov.: 32 AF XY: 0.487 AC XY: 36162 AN XY: 74286

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.493

Alfa AF: 0.492 Hom.: 10120

Bravo AF: 0.488

Asia WGS AF: 0.662 AC: 2304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.44

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: rs10062080; hg19: chr5-148660697;