rs11723068

Variant names:

• chr4-7795708-G-A
• rs11723068
• NM_001134647.2:c.1267-1882C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-7795708-G-A
• chr4-7795708-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

ENSG00000287164 (HGNC:58726):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134647.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFAP1	NM_001134647.2	MANE Select	c.1267-1882C>T		intron	N/A	NP_001128119.1	Q8N556-2
	AFAP1	NM_001371090.1		c.1267-1882C>T		intron	N/A	NP_001358019.1	Q8N556-1
	AFAP1	NM_001371091.1		c.1267-1882C>T		intron	N/A	NP_001358020.1	Q8N556-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFAP1	ENST00000420658.6	TSL:2 MANE Select	c.1267-1882C>T		intron	N/A	ENSP00000410689.1	Q8N556-2
	AFAP1	ENST00000360265.9	TSL:1	c.1267-1882C>T		intron	N/A	ENSP00000353402.4	Q8N556-1
	AFAP1	ENST00000382543.4	TSL:5	c.1267-1882C>T		intron	N/A	ENSP00000371983.3	Q8N556-2

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

African (AFR) AF: 0.0523 AC: 2161 AN: 41320

American (AMR) AF: 0.116 AC: 1763 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0561 AC: 194 AN: 3460

East Asian (EAS) AF: 0.481 AC: 2477 AN: 5150

South Asian (SAS) AF: 0.226 AC: 1079 AN: 4782

European-Finnish (FIN) AF: 0.157 AC: 1639 AN: 10460

Middle Eastern (MID) AF: 0.107 AC: 31 AN: 290

European-Non Finnish (NFE) AF: 0.0781 AC: 5296 AN: 67782

Other (OTH) AF: 0.106 AC: 223 AN: 2106

Alfa AF: 0.0856 Hom.: 588

Bravo AF: 0.0924

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-1.3
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: rs11723068; hg19: chr4-7797435;