4-7795708-G-A

Position:

• chr4-7795708-G-A

Variant summary

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

The NM_001134647.2(AFAP1):​c.1267-1882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 151,486 control chromosomes in the GnomAD database, including 1,261 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 0.099 (1261 hom., cov: 30)
• Consequence: AFAP1 NM_001134647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

AFAP1 (HGNC:24017): (actin filament associated protein 1) The protein encoded by this gene is a Src binding partner. It may represent a potential modulator of actin filament integrity in response to cellular signals, and may function as an adaptor protein by linking Src family members and/or other signaling proteins to actin filaments. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AFAP1	NM_001134647.2	c.1267-1882C>T		intron_variant		ENST00000420658.6	NP_001128119.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AFAP1	ENST00000420658.6	c.1267-1882C>T		intron_variant		2	NM_001134647.2	ENSP00000410689

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 14933 AN: 151372 Hom.: 1264 Cov.: 30

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0561

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0986 AC: 14930 AN: 151486 Hom.: 1261 Cov.: 30 AF XY: 0.106 AC XY: 7869 AN XY: 74064

Gnomad4 AFR AF: 0.0523

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0561

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.0781

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0877 Hom.: 405

Bravo AF: 0.0924

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.67

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: rs11723068; hg19: chr4-7797435;