chr4-7929955-A-C

Position:

• chr4-7929955-A-C

Variant summary

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

The NM_001134647.2(AFAP1):​c.-3+9701T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,096 control chromosomes in the GnomAD database, including 7,882 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 0.29 (7882 hom., cov: 33)
• Consequence: AFAP1 NM_001134647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AFAP1	NM_001134647.2	c.-3+9701T>G		intron_variant		ENST00000420658.6	NP_001128119.1
AFAP1	NM_001371091.1	c.-781+9701T>G		intron_variant			NP_001358020.1
AFAP1	NM_198595.3	c.-3+9701T>G		intron_variant			NP_940997.1
AFAP1	XM_006713909.4	c.61+8637T>G		intron_variant			XP_006713972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AFAP1	ENST00000420658.6	c.-3+9701T>G		intron_variant		2	NM_001134647.2	ENSP00000410689
AFAP1	ENST00000358461.6	c.-3+9701T>G		intron_variant		2		ENSP00000351245	P1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44492 AN: 151978 Hom.: 7886 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.293 AC: 44511 AN: 152096 Hom.: 7882 Cov.: 33 AF XY: 0.285 AC XY: 21213 AN XY: 74334

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.322

Alfa AF: 0.359 Hom.: 5400

Bravo AF: 0.280

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11930623; hg19: chr4-7931682;